Compositions and Methods for Suppressing MSUT2

ABSTRACT

Described herein are compositions and methods for treating Alzheimer&#39;s disease or dementia. The compositions include mammalian suppressor of taupathy 2 inhibitors (MSUT2). The MSUT2 inhibitors can be small interfering RNAs, guide RNAs, or small molecules. The methods include reducing accumulation of phosphorylated and aggregated human tau.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 16/383,178, which was filed Apr. 12, 2019, which claims the benefit of the filing date of U.S. Provisional Application No. 62/656,900, which was filed on Apr. 12, 2018. The content of these earlier filed applications are hereby incorporated by reference herein in its entirety.

STATEMENT REGARDING FEDERALLY FUNDED RESEARCH

This invention was made with government support under grant number 5I01BX000877 awarded by the Department of Veterans Affairs and under grant number RF1AG055474 awarded by National Institutes of Health. The government has certain rights in the invention.

INCORPORATION OF THE SEQUENCE LISTING

The present application contains a sequence listing that was submitted via EFS-Web concurrent with the filing of the application, containing the file name “37759.0204U2_SL.xml” which is 53,248 bytes in size, created on Sep. 6, 2022, and is herein incorporated by reference in its entirety pursuant to 37 C.F.R. § 1.52(e)(5).

BACKGROUND

The molecular mechanisms underpinning neurodegenerative diseases include the cellular disruption of proteostasis. In Alzheimer's disease (AD), this disruption manifests as the deposition of amyloid plaques and neurofibrillary tangles (NFTs), the diagnostic pathological lesions of the disorder. While the mechanistic relationship between plaques and tangles remains unclear, abnormal tau and Aβ synergize to drive neurodegeneration in AD. A large body of evidence supports the idea of Aβ amyloid pathology initiating the disease process in AD. However, the discovery of tau mutations in frontotemporal lobar degeneration with tau inclusions (FTLD-tau) (P. Poorkaj, et al., Ann. Neurol. 43, 815-825 (1998); M. G. Spillantini, et al., Proc. Natl. Acad. Sci. U.S.A. 95, 7737-7741 (1998); L. N. Clark, et al., Proc. Natl. Acad. Sci. U.S.A. 95, 13103-13107 (1998); and M. Hutton, et al., Nature 393, 702-705 (1998)) demonstrates that tau pathology can cause neurodegeneration independent of amyloid plaques. Furthermore, tau pathology, not amyloid deposition, correlates with the severity of dementia in AD (L. M. Bierer, et al., Arch Neurol 52, 81-88 (1995). Thus, findings to date justify active investigation of the mechanistic underpinnings of both amyloid- and tau-mediated neurodegeneration in AD. Despite a diverse array of highly powered AD clinical trials targeting amyloid production, clearance, or deposition, none have been successful. Altogether, these observations suggest that tau-targeted therapies in conjunction with removal of amyloid may be required to achieve cognitive preservation when treating AD (M. R. Khanna, et al., Alzheimers Dement 12, 1051-1065 (2016); and C. Ballatore, et al., Nat Rev Neurosci 8, 663-672 (2007)).

SUMMARY

Disclosed herein are methods of treating Alzheimer's disease or dementia, the methods comprising: administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor, wherein the therapeutically effective amount reduces accumulation of phosphorylated and aggregated human tau.

Disclosed herein are methods of inhibiting expression of a MSUT2 polynucleotide in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of inhibiting expression of a MSUT2 polynucleotide, the methods comprising contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor, wherein the suppressor of tauopathy 2 (MSUT2) reduces accumulation of phosphorylated and aggregated tau.

Disclosed herein are methods of reducing phosphorylated and aggregated human tau protein in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of suppressing expression of a MSUT2 polynucleotide in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of suppressing expression of a MSUT2 polynucleotide, the methods comprising contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor, wherein the suppressor of tauopathy 2 (MSUT2) reduces accumulation of phosphorylated and aggregated tau.

Disclosed herein are methods of potentiating a neuroinflammatory response to a pathological tau protein in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of potentiating a neuroinflammatory response to a pathological tau protein, the methods comprising contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor, wherein the suppressor of tauopathy 2 (MSUT2) reduces accumulation of phosphorylated and aggregated tau.

Disclosed herein are methods of decreasing astrocytosis or microgliosis in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of decreasing astrocytosis or microgliosis, the methods comprising contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor, wherein the suppressor of tauopathy 2 (MSUT2) reduces accumulation of phosphorylated and aggregated tau.

Disclosed herein are methods of reducing neuroinflammation in a subject, the methods comprising administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

Disclosed herein are methods of reducing neuroinflammation, the methods comprising contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor wherein the suppressor of tauopathy 2 (MSUT2) reduces accumulation of phosphorylated and aggregated tau.

Disclosed herein are guide RNA (gRNA) molecules that target one or more nucleotides in a MSUT2 gene.

Disclosed herein are CRISPR-Cas systems comprising one or more vectors comprising: a) a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA), wherein the gRNA hybridizes with a target sequence of a DNA locus in a cell; and b) a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease, wherein components a) and b) are located on the same or different vectors of the same system, wherein the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA locus; wherein the gRNA sequence is selected from the group consisting of SEQ ID NOs: 6, 7, 8, 9, 28, 29, 30, 31, 32 and 33. Disclosed herein are CRISPR-Cas systems comprising one or more vectors comprising: a) a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA), wherein the gRNA hybridizes with a target sequence of a DNA locus in a cell; and b) a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease, wherein components a) and b) are located on the same or different vectors of the same system, wherein the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA locus; wherein the gRNA sequence comprises 10-30 bp, 15-25 bp, 17-24 bp or any other fragment of the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33. In some aspects, the gRNA sequence comprises a sequence having 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, 33 or a fragment thereof.

Disclosed herein are vectors comprising: a) a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA); and b) a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease; wherein the gRNA sequence is selected from the group consisting of SEQ ID NOs: 6, 7, 8, 9, 28, 29, 30, 31, 32 and 33.

Disclosed herein are methods of screening for compounds capable of inhibiting MSUT2 binding to poly(A) RNA, the methods comprising: (a) contacting at least one candidate compound, poly(A) RNA and PABPN1 under conditions in which PABPN1 is capable of stimulating RNA polyadenylation in the absence of the candidate compound; (b) determining whether the candidate compound inhibits MSUT2 binding to poly(A) RNA; and (c) selecting the candidate compound which inhibits MSUT2 binding to poly(A) RNA.

Disclosed herein are methods for screening compounds for pharmacological intervention in tauopathy disorders, the methods comprising: (a) providing an assay for MSUT2 to bind to poly(A) RNA and its modulation of RNA polyadenylation; (b) providing a purified or non-purified compound or purified or non purified mixture of compounds; (c) screening the purified or non-purified compound or purified or non-purified mixture of compounds in an environment that allow for inhibition of MSUT2 binding to poly(A) RNA by the purified or non-purified compound or purified or non-purified mixture of compounds in the assay; and (d) isolating the one or more compounds that inhibit MSUT2 binding to poly(A) RNA.

Disclosed herein are compositions comprising a small molecule consisting of

-   -   wherein the composition reduces accumulation of phosphorylated         and aggregated human tau protein in a subject with Alzheimer's         disease or dementia.

Disclosed herein are compositions comprising a gRNA sequence selected from the group consisting of

(SEQ ID NO: 6) GAAUUUAUCGACCACCUGCAAGCAAAGUUUUAGUA CUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAU GCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUU UU, (SEQ ID NO: 7) GGCCUGCCUGUAAAAAUGGGGCAAAGUUUUAGUAC UCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUG CCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUU U, (SEQ ID NO: 8) GCCACCAAGACACGCCUUGAACAAAGUUUUAGUAC UCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUG CCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUU U, (SEQ ID NO: 9) AUUAGACACUUCAGAUAGAUCUGUUUUAGAGCUAG AAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCA ACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU, (SEQ ID NO: 33) GUACUGGCCUGCCUGUAAAAAUCAAAGUUUUAGUA CUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAU GCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUU UU, (SEQ ID NO: 28) GAAUUUAUCGACCACCUGCAAG (SEQ ID NO: 29) GUACUGGCCUGCCUGUAAAAAU (SEQ ID NO: 30) GGCCUGCCUGUAAAAAUGGGG (SEQ ID NO: 31) GCCACCAAGACACGCCUUGAA, and (SEQ ID NO: 32) AUUAGACACUUCAGAUAGAU.

Disclosed herein are compositions comprising

(SEQ ID NO: 10) AUGAUGCAAAGUGUACUAAACCAG, (SEQ ID NO: 11 AUGAUGCAAAGUGUACUAAACCAGAUU, (SEQ ID NO: 12) AUGAUGCAAAGUGUACUAAACCAGAU (SEQ ID NO: 13) AUGAUGCAAAGUGUACUAAACCA (SEQ ID NO: 14) AUAUGAUGCAAAGUGUACUAAACCAG, or (SEQ ID NO: 15) UAUGAUGCAAAGUGUACUAAACCAG.

Other features and advantages of the present compositions and methods are illustrated in the description below, the drawings, and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-F show MSUT2 KO mouse characterization. FIG. 1A shows the genetrap insertion site on mouse chromosome 12. Vertical bars are exons, intervening lines represent introns. The position on chromosome 12 is at 49.88 cM, cytoband F1 or between bases 98746968-98787774. The triangle on the lower diagram indicates the position of the deleted exon 13 in MSUT2 (otherwise known as ZC3H14). FIG. 1B shows the protein domain structures of mouse MSUT2 and C. elegans sut-2 homologs. Below is the consequence of deleting MSUT2 exon 13 for protein coding potential of the gene. Namely, the CCCH finger domains are deleted and out of frame resulting in a non-functional protein. Arrows with bk741 and bk87 indicate the locations of mutations identified in C. elegans that result in early stop codons. FIG. 1C shows the Northern blot of MSUT2 mRNA with an exon 13 specific probe. Note missing specific transcripts in MSUT2 KO mice (marked by arrowheads). FIG. 1D shows MSUT2 immunoblot for MSUT2 protein reveals loss of full MSUT2 protein isoforms in MSUT2 KO mice. MSUT2/ZC3H14 antibody recognizes the N-terminal domain which is not deleted by elimination of Exon 13 (J. Rha, et al., Hum Mol Genet, (2017)). FIG. 1E shows that MSUT2 KO show no change in total tau protein levels by immunoblot in PS19 Tg mice. Actin is load control. FIG. 1F shows that MSUT2 KO decreases accumulation of NFTs in the entorhinal cortex (EC) of PS19 tauopathy mice. NFTs are detectable by Gallyas silver stain of 9 month old PS19 tauopathy mouse brain sections. Gallyas+NFTs in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of ˜73% (p=0.0145 by two-tailed t-test). Scale bar=100 μm.

FIGS. 2A-E show Genetic ablation of MSUT2 protects against tauopathy in mice. FIG. 2A shows that MSUT2 KO decreases accumulation of NFTs in the CA1 region of hippocampi of PS19 tauopathy mice. NFTs are detectable by Gallyas silver stain of 9 month old PS19 tauopathy mouse brain sections. Gallyas+ NFT counts in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of 85% (p=0.0129 by two-tailed t-test). Statistical significance indicated by asterisks throughout the figures; * denotes p<0.05, ** denotes p<0.01, *** denotes p<0.001. Scale bar=100 μm. FIG. 2B shows that MSUT2 KO decreases accumulation of hyperphosphorolated tau (pTau) in the stratum lacunosum molecular (SLM) of PS19 tauopathy mice. pTau (T231) was detected by monoclonal antibody AT180 staining of 9 month old PS19 tauopathy mouse brain sections. Densitometry of AT180+ pathological tau deposits in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of 55% (p=0.0156 by two-tailed t-test). Scale bar=100 μm. FIG. 2C shows that MSUT2 KO decreases accumulation of pre-tangle tau species in the stratum oriens (SO) region of hippocampi of PS19 tauopathy mice. Pre-tangle pathological tau species were detected by conformation dependent tau monoclonal antibody MC1 staining of 9 month old PS19 tauopathy mouse brain sections. Densitometry of MC1+ lesions in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of 50% (p=0.0042 by two-tailed t-test). Scale bar=50 μm. FIG. 2D shows that MSUT2 KO decreases loss of CA1 region neurons of PS19 tauopathy mice. Neuronal cell bodies were detected by cresyl violet staining of 9 month old PS19 tauopathy mouse brain sections (arrows indicate pyramidal cell layer). Densitometry of pyramidal neuron density in MSUT2 KO/PS19 Tg (N=21) compared with PS19 Tg alone (N=19) demonstrated a significant increase in CA1 neurons of 53% (p=0.0062 by two-tailed t-test). FIG. 2E shows that MSUT2 KO enhances performance in Barnes maze training of 8 month old PS19 tauopathy mice. Although PS19 Tg+ animals perform poorly on the Barnes maze, taking longer to locate the escape hole compared to either WT or Msut2 KO animals (p<0.001), PS19 Tg+ animals that are homozygous for Msut2 KO perform much better (p<0.001), and are not significantly different from WT. Note normal spontaneous activity levels in both PS19 and MSUT2 KO/PS19 as measured in an open field (FIG. 4A), and normal locomotor coordination as measured on a rotorod (FIG. 4G).

FIGS. 3A-C show that MSUT2 KO decreases accumulation of pathological tau. FIG. 3A shows that MSUT2 KO decreases pTau in in the stratum oriens (SO) and entorhinal cortex (EC) of PS19 tauopathy mice. pTau (T231) was detected by phospho-dependent tau monoclonal antibody AT180 staining of 9 month old PS19 tauopathy mouse brain sections. Densitometry of AT180+ pathological tau deposits in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of 56% in the EC (p=0.01 by two-tailed t-test). The significant decrease in the SO was 56% (p=0.005 by two-tailed t-test). Scale bar=50 μm SO; 100 μm EC. FIG. 3B show that MSUT2 KO decreases accumulation of pre-tangle tau species in the stratum lacunosum molecular (SLM) region of hippocampus and the entorhinal cortex (EC) of PS19 tauopathy mice. Pre-tangle pathological tau species were detected by conformation dependent tau monoclonal antibody MC1 staining of 9 month old PS19 tauopathy mouse brain sections. Densitometry of MC1+ lesions in MSUT2 KO/PS19 Tg (N=24) compared with PS19 Tg alone (N=24) demonstrated a significant reduction of 43% in the EC (p=0.03 by two-tailed t-test). The decrease of 38% in the SLM approached statistical significance (p=0.07 by two-tailed t-test). Scale bar=100 μm. FIG. 3C shows that WT and MSUT2 KO mouse brain have similar NeuN staining throughout the hippocampus. Scale bar=500 μm.

FIGS. 4A-G show that MSUT2 KO mice have grossly normal cognitive and locomotor abilities. FIG. 4A shows that the animals at the time of Barnes testing remain active in an open field. The genotypes exhibit mild hyperactivity compared to wildtype when allowed to explore an open field for 10 minutes. Data are shown as mean +/−SEM. FIG. 4B shows that Msut2 KO mice have similar body weight compared to their wildtype littermates at 3 months (p=0.74). N=12 MSUT2 KO mice and N=7 WT controls. FIG. 4C shows that there is a strong effect of the PS19 transgene on body weight change from 6 to 9 months of age (p<0.001). FIG. 4D shows that there is not a significant main effect of MSUT2 genotype (p=0.18) on weight change from 6 to 9 months of age in PS19 animals, but there is a significant main effect of sex (p<0.0001) and an interaction between genotype and sex (p=0.05). Post-hoc analysis revealed a significant effect of MSUT2 genotype in males (p=0.02) but not in females (0.65). MSUT2 KO partially protects PS19 males against the weight loss associated with the tau transgene. PS19 females held approximately constant body weight from 6 to 9 months of age regardless of MSUT2 genotype. FIG. 4E shows that prior to progression to paralysis, PS19 Tg+ animals perform better than their non-Tg littermates on the rotorod task, in agreement with reports from other groups (p<0.001). FIG. 4F shows that Msut2 KO mice do not exhibit any locomotor defects during rotorod testing. (p=0.30). FIG. 4G shows that Msut2 KO did not have any significant effect on the locomotor coordination of PS19 Tg+ mice during rotorod testing. (p=0.54).

FIGS. 5A-E show that MSUT2 binds independently to both poly(A) tails and PABPN1. FIG. 5A shows the in vitro confirmation of the yeast two-hybrid interaction between MSUT2 CCCH finger domain and PABPN1. 35S radiolabeled PABPN1 was tested against immobilized recombinant GST-MSUT2 Zinc Finger (ZF) fusion protein or recombinant GST alone using GST pulldown assays. RNAse pre-treatment of samples does not prevent MSUT2 and PABPN1 protein-protein interactions. FIG. 5B shows that the Proximity Ligation Assay (PLA) detects MSUT2/PABPN1 interaction within intact HEK293 cell nuclei. Gray, DAPI staining. White, PLA detected interactions. Left, panel is high magnification stitched-panel image of a large field of PLA immunostained HEK293 cells. Scale bar=100 Rectangle represents a single image in the stitched panel. FIG. 5C shows the Surface Plasmon Resonance detection of MSUT2 and PABPN1 binding to poly(A) RNA. Dissociation constants were calculated for biotinylated poly(A)15 from the binding kinetics of each protein at five concentrations (1, 0.9, 0.8, 0.7, 0.6 1,IM). MSUT2 KD=60±15 nM vs PABPN1 KD=237±21 nM for poly(A)15. FIG. 5D shows that MSUT2 and PABPN1 colocalize in splicing factor SC35-positive nuclear speckles in HEK293 cells (Pearson Coefficient of Correlation (PCC)=0.7976). Representative single channel image of nuclear MSUT2, PABPN1, and DAPI. Colocalization analysis of MSUT2 with SC35 (PCC=0.7578) and PABPN1 with SC35 (PCC=0.4347) are shown in FIGS. 6C-D. FIG. 5E shows that MSUT2 and PABPN1 colocalize at nuclear speckles in neuronal nuclei from human frontal cortex. Representative confocal image shows immunofluorescent staining for MSUT2 (upper panel with box), PABPN1 (light white), and DAPI (gray). Inset image is high magnification examination of a single nucleus displayed as split channels for MSUT2 and PABPN1 and merged channels. MSUT2 and PABPN1 colocalize with a PCC=0.88 in this image (see also FIG. 6 ). Scale bar=25 μm.

FIGS. 6A-D show that MSUT2, PABPN1, and poly(A) mRNA colocalize at nuclear speckles in HEK293 cells. Representative images are displayed as split channels, merged, the colocalization of the two species, and the plot of the PCC of the two species. FIG. 6A shows that MSUT2 colocalizes with poly(A) mRNA within the nucleus with a PCC=0.7644. FIG. 6B shows that PABPN1 colocalizes with poly(A) mRNA with a PCC=0.6241. FIG. 6C shows that MSUT2 colocalizes with SC35 with a PCC=0.7578. FIG. 6D shows that less PABPN1 colocalizes with SC35 when compared to MSUT2 with a PCC=0.4347.

FIGS. 7A-J show that MSUT2 mediates effects on tauopathy through poly(A) tail length but not gene expression. FIG. 7A show that synthetic siRNA treatment eliminates MSUT2 and PABPN1 protein in HEK293 cells. FIG. 7B shows HEK/tau cells overexpressing human tau. Immunofluorescent staining of nuclei (DAPI, dark gray) and pTau T231 (AT180, white) (M. Goedert, et al., Biochem J 301 (Pt 3), 871-877 (1994)); positive staining control, total tau (light gray). Scale bar=15 nm. FIG. 7C shows that MSUT2 knockdown by siRNA decreases pTau accumulation. Immunofluorescent staining of nuclei (DAPI, dark gray) and pTau T231 (AT180) ((M. Goedert, et al., Biochem J 301 (Pt 3), 871-877 (1994)); positive staining control, total tau (light gray). FIG. 7D shows that PABPN1 knockdown by siRNA increases pTau accumulation. Immunofluorescent staining of nuclei (DAPI, dark gray) and pTau T231 (AT180, white) ((M. Goedert, et al., Biochem J 301 (Pt 3), 871-877 (1994)); positive staining control, total tau (light gray). FIG. 7E shows quantitation of immuno staining for pTau T231 (AT180), conformation dependent tau (MC1) (C. L. Weaver, et al., Neurobiology of Aging 21, 719-727 (2000)), and tau oligomeric complex-1 monoclonal antibody (TOC1) (S. M. Ward, et al., J Alzheimers Dis 37, 593-602 (2013); and K. R. Patterson, et al., Biochemistry 50, 10300-10310 (2011)). Error bars are SEM. For comparisons of MSUT2 siRNA treated to untreated cells stained for AT180, p<0.005, for PABPN1 treated vs untreated p<0.001; for TOC1 staining, MSUT2 siRNA vs untreated gives p<0.05, for PABPN1 treated vs untreated p<0.001; for both PABPN1 and MSUT2 treatment MC1 staining comparison vs untreated gives p<0.001. FIG. 7F shows that modulating poly(A) tail length exacerbates tauopathy. The ccr-4 mutants have long poly(A) tails on bulk mRNA. 4-day-old tau Tg C. elegans with or without a strong loss of function mutation in ccr-4 were placed in liquid and their swimming activity recorded. Tau Tg animals exhibit significantly better locomotion relative to tau Tg; ccr-4 mutant animals (p<0.0001 by 2-tailed Student's t-test). FIG. 7G shows multidimensional scaling and principal component analysis of MSUT2 KO vs. C57BL/6J RNA sequencing data. Total brain RNA from MSUT2 KO and C57BL/6J was analyzed by RNAseq. Principal component analysis clearly distinguishes knockout (ko) from control (ctl) mice. FIG. 7H shows the transcriptomic changes of MSUT2 KO vs. C57BL/6J from RNA sequencing data (normalized mean read count by gene). Differentially regulated genes are depicted as red spots. See Table 1 for listing of the differentially expressed genes. FIG. 7I shows the alternative splicing changes of MSUT2 KO vs. C57BL/6J from RNA sequencing data (normalized mean read count by exon). 201 differentially spliced exons were detected (depicted by gray spots). See FIG. 16 for listing of differentially spliced exons. FIG. 7J shows the volcano plot of alternative polyadenylation site selection (APA) changes in MSUT2 KO vs. C57BL/6J from RNA sequencing data. Analysis of APA was conducted using Dynamic Analysis of Alternative Polyadenylation from RNAseq (DaPars). Ten genes exhibited a significant change in percentage of distal poly(A) site usage (PDUI) of greater than 20% (see gray spots). See FIG. 17 for listing of genes with significant alterations in APA.

FIGS. 8A-C show that MSUT2 and PABPN1 have opposing impacts on tau aggregation, but MSUT2 KO in mice does not influence PABPN1 levels. FIG. 8A shows that tau protein was sequentially extracted to obtain detergent insoluble tau protein from HEK/tau cells with or without MSUT2 and PABPN1 siRNA knockdown. MSUT2 knockdown ameliorates aggregated tau accumulation while PABPN1 knockdown exacerbates tau aggregation. Knockdown of both MSUT2 and PABPN1 together has an intermediate effect on tau aggregation. The detergent insoluble fraction containing aggregated tau was probed with a pan-tau antibody as described (see ab17026 (68)). FIG. 8B shows that comparison of PABPN1 protein levels in PS19 Tg and PS19/MSUT2 KO mice as determined by immunoblotting. FIG. 8C shows the comparison of PABPN1 expression in wild type vs. MSUT2 KO mice by PABPN1 immunohistochemistry (IHC).

FIGS. 9A-F show MSUT2 overexpression in the hippocampus following AAV-MSUT2 injection. MSUT2 overexpression is seen throughout the hippocampal formation on the ipsilateral side (FIG. 9A) compared to the contralateral side (FIG. 9B) of the brain of Tau4RTg2652 mice injected with AAV-MSUT2. FIGS. 9C, 9D show higher magnification of the CA3 region of the hippocampus. Note that MSUT2 is normally expressed in the nucleus of CA3 neurons on the contralateral side (FIG. 9D) but is abnormally distributed to the cytoplasm and fibers on the ipsilateral side when overexpressed by AAV injection. FIG. 9E shows that MSUT2 overexpression does not impact tau abundance. Shown is the hippocampus of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP and immunostained for total tau. FIG. 9F shows that MSUT2 overexpression increases microgliosis. Shown is the ipsilateral fimbria of the hippocampus of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates reactive microglia as compared to AAV-GFP injection. Microgliosis was detected by IBA1 IHC of glia by staining of 4 month old Tau4RTg2652 tauopathy mouse brain sections. Densitometry of IBA1+ reactivity in MSUT2 AAV/Tg2652 (N=12) compared with GFP AAV/Tg2652 (N=5) demonstrated an increase of 1816% that approached statistical significance (p=0.06 by two-tailed t-test). Scale bars=500 μm (A, B) 50 μm (C, D) 100 μm (E).

FIGS. 10A-E shows MSUT2 potentiates neuroinflammation, tau pathology and neurodegeneration. FIG. 10A shows that MSUT2 overexpression exacerbates pTau accumulation in hippocampus. Shown is the ipsilateral CA1 region of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates pTau accumulation as compared to AAV-GFP injection. pTau (phospho-Thr231) was detected by phospho-dependent tau monoclonal antibody AT180 staining of 4 month old Tau4RTg2652 tauopathy mouse brain sections (arrows indicate CA1 pyramidal cell layer). Densitometry of AT180+ pathological tau deposits in MSUT2 AAV/Tau4RTg2652 (N=15) compared with GFP AAV/Tau4RTg2652 (N=5) demonstrated a significant increase of 294% (p=0.0044 by two-tailed t-test). Scale bar=100 μm. FIG. 10B shows that MSUT2 overexpression exacerbates neuronal loss in hippocampus. Shown is the ipsilateral CA3 region of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates neuronal loss in CA3 as compared to AAV-GFP injection. Neuronal cell bodies were detected by cresyl violet staining (arrows indicate CA3 pyramidal cell layer). Densitometry of pyramidal layer staining in MSUT2 AAV/Tau4RTg2652 (N=15) compared with GFP AAV/Tau4RTg2652 (N=5) demonstrated a significant decrease of cresyl violet positive neuronal cell bodies in CA3 (33%, p=0.0001 by two-tailed t-test). Scale bar=100 μm. FIG. 10C shows that MSUT2 overexpression exacerbates microgliosis in hippocampus. Shown is the ipsilateral CA3 region of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates reactive microglia as compared to AAV-GFP injection. Microgliosis was detected by IBA1 IHC of glia by staining of 4-month-old Tau4RTg2652 tauopathy mouse brain sections. Densitometry of IBA1+ reactivity in MSUT2 AAV/Tg2652 (N=13) compared with GFP AAV/Tau4RTg2652 (N=5) demonstrated a statistically significant 19-fold increase (p=0.024 by two-tailed t-test). Scale bar=100 μm. FIG. 10D shows that MSUT2 overexpression exacerbates astrocytosis in hippocampus. Shown is the ipsilateral CA3 region of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates reactive astrocytes as compared to AAV GFP injection. Astrocytosis was detected as GFAP reactivity of astrocytes by immunostaining of 4 month old Tau4RTg2652 tauopathy mouse brain sections. Densitometry of GFAP+ reactivity in MSUT2 AAV/Tg2652 (N=14) compared with GFP AAV/Tau4RTg2652 (N=5) demonstrated a statistically significant 12-fold increase (p=0.022 by two-tailed t-test). Scale bar=100 μm. FIG. 10E shows that MSUT2 KO suppresses reactive astrocytosis in response to tau pathology in PS19 mice. Shown is the entorhinal cortex of PS19 Tg mice analyzed for astrocytosis by IHC for GFAP. Densitometry of GFAP+ reactivity in the EC of MSUT2 KO/PS19 Tg (N=23) compared with PS19 Tg alone (N=23) demonstrated an approximately 2-fold decrease in astrocytosis (p=0.0104 by two-tailed t-test). Scale bar=100 μm.

FIGS. 11A-B show the effect of MSUT2 expression on astrocytes in the hippocampus. FIG. 11A shows that MSUT2 overexpression increases astrocytosis. Shown is the ipsilateral fimbria of the hippocampus of Tau4RTg2652 mice injected with AAV-MSUT2 or AAV-GFP. MSUT2 overexpression exacerbates reactive astrocytes as compared to AAV-GFP injection. Astrocytosis was detected as GFAP reactivity of astrocytes by immunostaining of 4 month old Tau4RTg2652 tauopathy mouse brain sections. Densitometry of GFAP+ reactivity in MSUT2 AAV/Tg2652 (N=14) compared with GFP AAV/Tg2652 (N=5) demonstrated a significant increase of 468% (p=0.011 by two-tailed t-test). FIG. 11B shows that MSUT2 KO suppresses reactive astrocytosis in response to tau pathology in PS19 mice. Shown are the stratum oriens (SO) and stratum lacunosum molecular (SLM) regions of the hippocampi of PS19 Tg mice analyzed for astrocytosis by IHC for GFAP. Densitometry of GFAP+ reactivity in the SO and SLM of MSUT2 KO/PS19 Tg (N=24) was compared with PS19 Tg alone (N=23), demonstrating a significant decrease in astrocytosis (˜43% in SO, p=0.011 by two-tailed t-test; ˜35% in SLM, p=0.021 by two-tailed t-test). CA1 and stratum radiatum (SR) are indicated for orientation. Scale bar=50 μm SO; 100 μm SLM and fimbria.

FIGS. 12A-D show that MSUT2 KO suppresses reactive microgliosis in response to tau pathology in PS19 mice. Shown are the (FIG. 12A) entorhinal cortex (EC), (FIG. 12B) stratum oriens (SO), and (FIG. 12C) stratum lacunosum molecular (SLM) of PS19 Tg mice analyzed for microgliosis by IHC for Iba1. Densitometry of Iba1+ reactivity in MSUT2 KO/PS19 Tg (N=23) was compared with PS19 Tg alone (N=24) in microgliosis. While there was a trend for reduced microgliosis in the three regions, this difference did not reach statistical significance. Scale bar=50 μm SO; 100 μm SLM and EC. FIG. 12D shows that post mortem interval (PMI) in hours for AD cases analyzed are not significantly different (p=0.25 by unpaired two tailed t-test).

FIG. 13 shows that MSUT2 KO does not alter astrocytosis in response to Kainic Acid (KA) exposure. Shown are the hippocampi of wild type or MSUT2 KO mice 3 days after KA treatment (a single dose of 25 mg/kg KA administered i.p.). While KA treatment provoked an obvious and strong gliotic response, there is no obvious difference in MSUT2 KO relative to wildtype littermates in terms of astrocytosis (IHC for GFAP) in response to KA treatment. Scale bar=500 μm.

FIGS. 14A-I show that MSUT2 activity potentiates neuroinflammation induced by tauopathy. FIG. 14A shows that AD brain frontal cortex co-immunostained for pathological tau (gray) and MSUT2 (white) reveals MSUT2-positive neurons harboring tangles. Pathological tau is detected by immunofluorescence with mAb AT180 (M. Goedert, et al., Biochem J 301 (Pt 3), 871-877 (1994)) while MSUT2 is detected with a polyclonal MSUT2 antibody (C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011)). Arrow on inset panel indicates an MSUT2+ tangle bearing neuron. Scale bar=100 nm. FIG. 14B shows that MSUT2 immunostaining on normal control and AD cortex brain sections indicates MSUT2 protein is abundant in normal controls and some AD cases, while other AD cases have depleted or completely undetectable MSUT2 protein. See Table 4 for AD case series details. Scale bar=50 nm. FIG. 14C shows that PABPN1 immunostaining on normal control and AD cortex brain sections shows PABPN1 protein is abundant in normal controls and some AD cases, while other AD cases have greatly reduced PABPN1. Scale bar=50 nm. FIG. 14D shows that postmortem AD frontal cortex analysis of MSUT2 levels as a function of age at disease onset (see Table 4 for case details). AD cases with normal MSUT2 (N=14) have a later age of onset as compared with cases with depleted MSUT2 (N=13) (p=0.0306 by Student's t-test). FIG. 14E shows the analysis of PABPN1 levels as a function of age at onset of AD in postmortem tissue (see Table 4 for case details). AD cases with normal PABPN1 (N=16) have a later age of onset as compared with cases with depleted PABPN1 (N=11) (p=0.0084 by Student's t-test). FIG. 14F shows that PABPN1 and MSUT2 levels may influence severity of astrocytosis in AD. Evaluation of astrocytosis in the frontal cortex of AD cases with PABPN1 and MSUT2 complex normal (PMC+) vs. depleted (PMC Depleted) stained with GFAP specific antibody. Densitometry of GFAP-positive reactivity in PMC+ cases (N=9) compared with PMC depleted cases (N=6) demonstrated a significant decrease of over 400% (p=0.0139 by two-tailed t-test). Scale bar=50 nm. FIG. 14G show that PABPN1 and MSUT2 levels may influence severity of microgliosis in AD. Evaluation of microgliosis in the frontal cortex of AD cases with normal MSUT2 (PMC+) vs depleted MSUT2 (PMC Depleted) stained with IBA1 specific antibody. Densitometry of IBA1+ reactivity in PMC normal cases (N=9) compared with PMC depleted cases (N=6) demonstrated a trend towards decrease in PMC depleted cases of 51.9% (p=0.069 by two-tailed t-test). Scale bar=50 nm. FIG. 14H show that the PABPN1 and MSUT2 complex (PMC) depleted AD cases exhibit more pathological tau (AT180+ lesions) than PMC+ cases. Densitometry of AT180-positive reactivity in PMC normal cases (N=14) compared with PMC depleted cases (N=13) demonstrated a significant increase of over 218% (p=0.0089 by two-tailed t-test). Scale bar=500 nm. FIG. 14I shows that the PABPN1 and MSUT2 complex (PMC) depleted AD cases exhibit more neuronal loss (less NeuN positive neurons) than PMC+ cases. Densitometry of NeuN-positive reactivity in PMC normal cases (N=14) compared with PMC depleted cases (N=13) demonstrated a significant increase of over 272% (p=0.0039 by two-tailed t-test). Scale bar=500 nm.

FIGS. 15A-B show the molecular hypothesis for MSUT2 activity. FIG. 15A shows a data summary. PS19 transgenic mice exhibit tau pathology in the form of misfolded tau and paired helical filaments. Tau pathology reduces tau binding to microtubules promoting microtubule destabilization and neurofibrillary degeneration. Pathological tau aggregation causes neurodegeneration driving gliosis and other neuroinflammatory changes. Knocking out MSUT2 in the PS19 tau transgenic mouse brain reduces pathological tau species, thereby protecting neurons and reducing consequent gliosis. Neurons (large cell), Microglia (small cell), Microtubules (MT-labeled striated bundle), Paired helical filaments (PHFs-black fibers), Tau (T). FIG. 15B shows a working hypothesis: MSUT2 and PABPN1 may act together in a complex and influence neuronal susceptibility to pathological tau. PABPN1 and MSUT2 form a complex binding to poly(A) in normal human brain, Alzheimer's disease, and PS19 Tg mice. The PABPN1/MSUT2 complex (PMC) could enable the development of tau pathology and the neuroinflammatory response to tau resulting in vulnerability of select neurons. Depletion of the PMC in severe AD accompanies more abundant tau pathology, disrupted MTs, and widespread neuronal loss with a paradoxical reduction in neuroinflammatory changes (dashed arrows indicate correlation not causation). Depletion of MSUT2 but sparing of PABPN1 in tau Tg mice promotes restoration of tau/microtubule homeostasis and neuroprotection resulting in suppression of neuroinflammation.

FIGS. 16A-M show MSUT2 KO vs C57BL/6 alternative exon inclusion changes.

FIGS. 17A-T show MSUT2 KO vs C57BL/6 alternative DaPars analysis of alternative polyadenylation usage.

FIGS. 18A-C show the summary of pilot AlphaScreen for antagonists of polyA RNA/MSUT2 protein interaction (FIG. 18A, FIG. 18B, and FIG. 18C).

FIG. 19 shows dose validated hits identified by AlphaScreen Assay. 1. Ebselen (IC50=1.6 μM); 2. Palmatine (IC50=1.7 μM); and 3,4,4′-Diisothiocyano-stilbene-2,2′ sulfonic acid (IC50=6.8 μM).

FIG. 20 shows Ebselen dose response in AlphaScreen Assay. (IC50=1.6 μM)

FIG. 21 shows validation funnel and secondary screening strategies.

FIG. 22 shows that MSUT2 and PABPN1 bind poly(A) RNA. RNA-protein affinities measured by surface plasmon resonance (BIACORE). MSUT2 K_(D) for poly(A) RNA=60±15 nM PABPN1 K_(D) for poly(A) RNA=237±21 nM.

FIG. 23 is a schematic of fluorescence polarization assay. Polarized light excites fluorescein labeled RNA molecule (FAM-PolyA₁₅). When bound to MSUT2 protein, it results in slow tumbling and emits polarized fluorescence. However, if this interaction is inhibited by a compound (i), it results in rapid tumbling of the unbound FAM-PolyA₁₅ and subsequent low polarization signal.

FIGS. 24A-D show the results of using the fluorescence polarization assay. FIG. 24A shows that increasing concentrations of MSUT2 protein result in increasing polarization signal. FIG. 24B shows that increasing concentrations of PABPN1 protein result in increased polarization signal. FIG. 24C shows that titration of unlabeled PolyA results in decrease of polarization signal. FIG. 24D shows that Compound A titration decreases fluorescence polarization signal.

DETAILED DESCRIPTION

Many modifications and other embodiments of the present disclosure set forth herein will come to mind to one skilled in the art to which this disclosure pertains having the benefit of the teachings presented in the foregoing descriptions and the associated drawings. Therefore, it is to be understood that the present disclosure is not to be limited to the specific embodiments disclosed and that modifications and other embodiments are intended to be included within the scope of the appended claims. Although specific terms are employed herein, they are used in a generic and descriptive sense only and not for purposes of limitation.

Before the present compositions and methods are disclosed and described, it is to be understood that they are not limited to specific synthetic methods unless otherwise specified, or to particular reagents unless otherwise specified, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular aspects only and is not intended to be limiting. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure, example methods and materials are now described.

Moreover, it is to be understood that unless otherwise expressly stated, it is in no way intended that any method set forth herein be construed as requiring that its steps be performed in a specific order. Accordingly, where a method claim does not actually recite an order to be followed by its steps or it is not otherwise specifically stated in the claims or descriptions that the steps are to be limited to a specific order, it is in no way intended that an order be inferred, in any respect. This holds for any possible non-express basis for interpretation, including matters of logic with respect to arrangement of steps or operational flow, plain meaning derived from grammatical organization or punctuation, and the number or type of aspects described in the specification.

All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited. The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present disclosure is not entitled to antedate such publication by virtue of prior disclosures. Further, the dates of publication provided herein can be different from the actual publication dates, which can require independent confirmation.

Definitions

As used in the specification and in the claims, the term “comprising” can include the aspects “consisting of” and “consisting essentially of” “Comprising” can also mean “including but not limited to.”

As used in the specification and the appended claims, the singular forms “a,” “an” and “the” can include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a compound” includes mixtures of compounds; reference to “a pharmaceutical carrier” includes mixtures of two or more such carriers, and the like.

The word “or” as used herein means any one member of a particular list and also includes any combination of members of that list.

As used herein, the terms “optional” or “optionally” mean that the subsequently described event or circumstance may or may not occur and that the description includes instances where said event or circumstance occurs and instances where it does not.

As used herein, the term “sample” is meant a tissue or organ from a subject; a cell (either within a subject, taken directly from a subject, or a cell maintained in culture or from a cultured cell line); a cell lysate (or lysate fraction) or cell extract; or a solution containing one or more molecules derived from a cell or cellular material (e.g. a polypeptide or nucleic acid), which is assayed as described herein. A sample may also be any body fluid or excretion (for example, but not limited to, blood, urine, stool, saliva, tears, bile) that contains cells or cell components.

As used herein, the term “subject” refers to the target of administration, e.g., a human. Thus the subject of the disclosed methods can be a vertebrate, such as a mammal, a fish, a bird, a reptile, or an amphibian. The term “subject” also includes domesticated animals (e.g., cats, dogs, etc.), livestock (e.g., cattle, horses, pigs, sheep, goats, etc.), and laboratory animals (e.g., mouse, rabbit, rat, guinea pig, fruit fly, etc.). In one aspect, a subject is a mammal. In another aspect, a subject is a human. The term does not denote a particular age or sex. Thus, adult, child, adolescent and newborn subjects, as well as fetuses, whether male or female, are intended to be covered.

As used herein, the term “patient” refers to a subject afflicted with a disease or disorder. The term “patient” includes human and veterinary subjects. In some aspects of the disclosed methods, the “patient” has been diagnosed with a need for treatment for Alzheimer's disease or dementia, such as, for example, prior to the administering step.

Ranges can be expressed herein as from “about” or “approximately” one particular value, and/or to “about” or “approximately” another particular value. When such a range is expressed, a further aspect includes from the one particular value and/or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” or “approximately,” it will be understood that the particular value forms a further aspect. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint and independently of the other endpoint. It is also understood that there are a number of values disclosed herein and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that each unit between two particular units is also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.

“Inhibit,” “inhibiting” and “inhibition” mean to diminish or decrease an activity, response, condition, disease, or other biological parameter. This can include, but is not limited to, the complete ablation of the activity, response, condition, or disease. This may also include, for example, a 10% inhibition or reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, in an aspect, the inhibition or reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels. In an aspect, the inhibition or reduction is 10-20, 20-30, 30-40, 40-50, 50-60, 60-70, 70-80, 80-90, or 90-100% as compared to native or control levels. In an aspect, the inhibition or reduction is 0-25, 25-50, 50-75, or 75-100% as compared to native or control levels.

“Modulate”, “modulating” and “modulation” as used herein mean a change in activity or function or number. The change may be an increase or a decrease, an enhancement or an inhibition of the activity, function or number.

As used herein, the term “treating” refers to partially or completely alleviating, ameliorating, relieving, delaying onset of, inhibiting or slowing progression of, reducing severity of, and/or reducing incidence of one or more symptoms or features of a particular disease, disorder, and/or condition. Treatment can be administered to a subject who does not exhibit signs of a disease, disorder, and/or condition and/or to a subject who exhibits only early signs of a disease, disorder, and/or condition for the purpose of decreasing the risk of developing pathology associated with the disease, disorder, and/or condition. Treatment can also be administered to a subject to ameliorate one more signs of symptoms of a disease, disorder, and/or condition. For example, the disease, disorder, and/or condition can be relating to Alzheimer's disease, Alzheimer's disease-related dementia or dementia.

The phrase “nucleic acid” as used herein refers to a naturally occurring or synthetic oligonucleotide or polynucleotide, whether DNA or RNA or a DNA-RNA hybrid, single-stranded or double-stranded, sense or antisense, which is capable of hybridization to a complementary nucleic acid by Watson-Crick base-pairing. Nucleic acids as disclosed herein can also include nucleotide analogs (e.g., BrdU), and non-phosphodiester internucleoside linkages (e.g., peptide nucleic acid or thiodiester linkages). In particular, nucleic acids can include, without limitation, DNA, RNA, cDNA, gDNA, ssDNA, dsDNA or any combination thereof.

As used herein, the term “complementary” refers to the ability of a nucleic acid to form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. A percent complementary indicates the percentage of residues in a nucleic acid molecule which can form hydrogen bonds (e.g., Wastson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary).

As used herein, the term “vector” or “construct” refers to a nucleic acid sequence capable of transporting into a cell another nucleic acid to which the vector sequence has been linked. The term “expression vector” includes any vector, (e.g., a plasmid, cosmid or phage chromosome) containing a gene construct in a form suitable for expression by a cell (e.g., linked to a transcriptional control element or regulatory element). The terms “plasmid” and “vector” can be used interchangeably, as a plasmid is a commonly used form of vector. Moreover, this disclosure is intended to include other vectors which serve equivalent functions.

All publications and patent applications mentioned in the specification are indicative of the level of those skilled in the art to which this invention pertains. All publications and patent applications are herein incorporated by reference to the same extent as if each individual publication or patent application was specifically and individually indicated to be incorporated by reference.

Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, certain changes and modifications may be practiced within the scope of the appended claims.

Abnormally aggregated highly phosphorylated tau becomes deposited as tangles or other lesions in tauopathy disorders. For Alzheimer's disease (AD) and many other tauopathies, the molecular role tau plays in disease initiation and progression remains unknown. However, in frontotemporal lobar degeneration-tau (FTLD-tau), mutations in the gene encoding tau (MAPT) cause the disease by reducing tau affinity for microtubules (MTs) and increasing tau aggregation propensity (M. Hong, et al., Science 282, 1914-1917 (1998); and S. Barghom, et al., Biochemistry 39, 11714-11721 (2000)). Because tau binds MTs, abnormal tau may impair function of the cytoskeleton. The reduced affinity of tau for MTs caused by FTLD mutations may disrupt MT stability and axonal transport (M. Hong, et al., Science 282, 1914-1917 (1998)). Alternately, tau aggregation may reduce the amount of tau available for binding to microtubules (M. R. Khanna, et al., Alzheimers Dement 12, 1051-1065 (2016); and V. M. Lee, et al., Neurobiol Aging 15 Suppl 2, S87-89 (1994)). Evidence suggests toxic tau aggregates or oligomers can spread by a seeding mechanism following neuronal connectivity pathways (H. Braak, et al., Neurobiol Aging 16, 271-278; discussion 278-284 (1995); and F. Clavaguera, et al., Nat Cell Biol 11, 909-913 (2009)). The important neurotoxic species remain poorly defined, and dimers, low level tau oligomers, higher order assemblies of tau, and end-stage NFTs are candidate triggers of neurotoxicity. The phosphorylation state of tau likely contributes to toxicity as tau phosphorylation can drive tau from MTs and promote aggregation (reviewed in (Y. Wang, et al., Nat Rev Neurosci 17, 5-21 (2016); and C. Ballatore, et al., Curr Top Med Chem 11, 317-330 (2011)). Taken together, recent evidence suggests a diversity of related and varyingly neurotoxic species likely contribute to both the spreading of tau pathology and tau-mediated neurodegeneration (reviewed in N. Sahara, et al., Curr Alzheimer Res 5, 591-598 (2008); and M. Goedert, Alzheimers Dement 12, 1040-1050 (2016)).

How abnormal tau kills neurons remains unknown. The identification of genes mediating susceptibility or resistance to pathological tau may inform disease mechanisms in AD and related disorders. To date, genomic studies in AD patients implicate many genes in susceptibility, however the APOE2 allele is strongly protective against AD. Among the risk-causing genetic variants, genes involved in innate immune response and expressed in microglia are unusually common (reviewed in (A. C. Naj, et al., Am J Med Genet B Neuropsychiatr Genet 174, 5-26 (2017)). While glial tau pathology does not commonly occur in AD, it is a feature of some pure tauopathy disorders (T. Komori, Brain Pathology 9, 663-679 (1999)) occurring in astrocytes in progressive supranuclear palsy (PSP) and in oligodendrocytes in some forms of FTLD. Furthermore, reactive gliosis is a common feature of tauopathy disorders including AD. Neuroinflammation and tau pathology appear to be mutually reinforcing features of AD and related disorders (N. Maphis, et al., Alzheimer's research & therapy 8, 54 (2016); N. Maphis, et al., Frontiers in neuroscience 9, 196 (2015); and K. Bhaskar, et al., Regulation of tau pathology by the microglial fractalkine receptor. Neuron 68, 19-31 (2010)).

To identify genes controlling tau toxicity, a tauopathy model was generated by expressing human tau in C. elegans using a promoter that drives expression in neurons. The phenotype of this model includes uncoordinated locomotion, accumulation of insoluble tau, neurodegeneration, and a shortened life span (B. C. Kraemer, et al., Proc Natl Acad Sci USA 100, 9980-9985 (2003)). This model was used to identify loss-of-function mutations suppressing tau-induced neurodegenerative phenotypes (C. R. Guthrie, et al., Hum Mol Genet 18, 1825-1838 (2009); and B. C. Kraemer, et al., Hum Mol Genet 16, 1959-1971 (2007)). In this model, loss-of-function mutations in the uppressor of tauopathy 2 gene (sut-2) decrease tau aggregation and protect against neurodegeneration (C. R. Guthrie, B. C. Kraemer, Proteasome inhibition drives HDAC6-dependent recruitment of tau to aggresomes. J Mol Neurosci 45, 32-41 (2011)). The sut-2 gene encodes a CCCH (SEQ ID NO: 22) finger protein with conserved homologs in species from yeast to humans. MSUT2 (also known as ZC3H14) is the mammalian homolog of the C. elegans sut-2 gene. As described herein, the loss of function of MSUT2 in mammals would ameliorate neurodegenerative tauopathy by a previously unknown mechanism. As disclosed herein, the mechanistic role of MSUT2 in resistance to tauopathy in mice and humans was examined.

Compositions

The compositions disclosed herein include a CRISPR-Cas system. The CRISPR-Cas system can be non-naturally occurring. In some aspects, the CRISPR-Cas system comprises one or more vectors. In an aspect, the vector can be a repression vector.

In some aspects, the one or more vectors can comprise a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA). In some aspects, the gRNA can hybridize with a target sequence of a DNA molecule or locus in a cell. In some aspects, the one or more vectors can also comprise a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease. In some aspects, the promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA and the regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease can be located on the same or different vectors of the same system. The gRNA can target and hybridize with the target sequence. In some aspects, the gRNA can also direct the RNA-directed nuclease into the DNA molecule or locus. In some aspects, gRNA can be selected from the group consisting of SEQ ID NOs: 6, 7, 8, 9, 28, 29, 30, 31, 32 and 33.

As used herein, the term “regulatory element” refers to promoters, promoter enhancers, internal ribosomal entry sites (IRES) and other elements that are capable of controlling expression (e.g., transcription termination signals, including but not limited to polyadenylation signals and polyuridylic acid sequences). Regulatory elements can direct constitutive expression. Regulatory elements can be tissue-specific. Examples of tissue-specific promoters can direct expression in a desired tissue of interest (e.g., neuron), specific organs (e.g., brain, spinal cord, liver), or particular cell types (neurons, microglia, astrocytes, oligodendrocytes, hepatocytes). Regulatory elements can also direct expression in a temporal-dependent manner including but not limited to cell-cycle dependent or developmental stage-dependent. Temporal-dependent expression can be tissue or cell-type specific. Regulatory element can also refer to enhancer elements. Examples of enhancer elements include but are not limited to woodchuck hepatitis post-transcriptional regulatory element (WPRE), human cytomegalovirus (CMV) enhancers, and simian virus 40 (SV40) enhancers. In an aspect, the regulatory element can be human Ubiquitin C (hUbC) promoter. In an aspect, the hUbC promoter is operably linked to a nucleotide sequence encoding a RNA-directed nuclease. Generally, any constitutive promoter can be operably linked to a nucleotide sequence encoding a RNA-directed nuclease. Gene specific promoters can be used. Such promoters allow cell specific expression or expression tied to specific pathways. Any promoter that is active in mammalian cells can be used. In an aspect, the promoter can be an inducible promoter including, but not limited to, tetracycline/doxycycline-controlled activation systems (also known as Tet-on Tet-off systems). Such inducible promoters can be used to control the timing of the desired expression.

Disclosed herein, are vectors comprising a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA and a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease. In some aspects, the gRNA sequence can be selected from the group consisting of SEQ ID NOs: 6, 7, 8, 9, 28, 29, 30, 31, 32 and 33. In an aspect, the gRNA sequence can comprise 10-30 bp, 15-25 bp, 17-24 bp or any other fragment of the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33. In some aspects, the gRNA sequence can comprise a sequence having 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, 33 or a fragment thereof. In some aspects, the gRNA sequence can comprise a sequence having 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 28, 29, 30, 31, 32 or a fragment thereof. In some aspects, any of the gRNA sequences or gRNA fragments disclosed herein can contain 1, 2, 3, or 4 or more nucleotide changes as compared to the parent or reference gRNA. Said sequences can share or improve biological function, specificity and/or activity of the parent or reference gRNA. In some aspects, any of gRNA sequences disclosed herein can include a single nucleotide change as compared to the parent or reference gRNA. In some aspects, any of the gRNA sequences disclosed herein can include at least two nucleotide changes as compared to the parent or reference gRNA. In some aspects, the gRNA fragment can include a deletion of at least one or at least two nucleotides at the 5′ end, the 3′end, or at both the 5′ and 3′end. In some aspects, the promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA and a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease can be on the same or different vectors of the same system.

Vectors include, but are not limited to nucleic acid molecules that are single-stranded double-stranded, or partially double-stranded; nucleic acid molecules that comprise one or more free ends, no free ends (e.g. circular); nucleic acid molecules that comprise DNA, RNA, or both; and other varieties of polynucleotides known in the art. One type of vector is a viral vector, wherein virally-derived DNA or RNA sequences are present in the vector for packaging into a virus. Viral vectors can include polynucleotides carried by a virus for transfection into a host cell. In some aspects, the CRISPR-Cas system described herein can be packaged into a single lentiviral, adenoviral or adeno-associated virus particle. In an aspect, the the CRISPR-Cas system can be packaged into a single adeno-associated virus particle.

The vectors disclosed herein can also include detectable labels. Such detectable labels can include a tag sequence designed for detection (e.g., purification or localization) of an expressed polypeptide. Tag sequences include, for example, green fluorescent protein, yellow fluorescent protein, red, fluorescent protein, mCherry, glutathione S-transferase, polyhistidine, c-myc, hemagglutinin, or Flag™ tag, and can be fused with the encoded nucleic acid. In some aspects, the vector can be pX601. In some aspects, the vector can be pX330. In some aspects, the vector can have a 3×hemagglutinin (HA) tag on the saCas9 (Staphylococcus aureus Cas9).

Some vectors are capable of autonomous replication in a host cell which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Other vectors (e.g., non-episomal mammalian vectors) are integrated into the genome of a host cell upon introduction into the host cell, and are thereby replicated along with the host genome.

The term “expression vector” is used herein to refer to vectors that are capable of directing the expression of genes to which they are operatively-linked. Common expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. Recombinant expression vectors can comprise a nucleic acid as disclosed herein in a form suitable for expression of the acid in a host cell. In other words, the recombinant expression vectors can include one or more regulatory elements or promoters, which can be selected based on the host cells used for expression that is operatively linked to the nucleic acid sequence to be expressed.

The term “operatively linked to” refers to the functional relationship of a nucleic acid with another nucleic acid sequence. Promoters, enhancers, transcriptional and translational stop sites, regulatory elements, regulatory control elements and other signal sequences are examples of nucleic acid sequences operatively linked to other sequences. For example, operative linkage of DNA to a transcriptional control element refers to the physical and functional relationship between the DNA and promoter such that the transcription of such DNA is initiated from the promoter by an RNA polymerase that specifically recognizes, binds to and transcribes the DNA.

One or more vectors can be introduced into a cell (e.g., a host cell) to produce transcripts, proteins, peptides including fusion proteins and peptides, encoded by nucleic acids as described herein (e.g., clustered regularly interspersed short palindromic repeats (CRISPR) transcripts, proteins, enzymes, mutant forms thereof, fusion proteins thereof, etc.). In some aspects, the vector is a viral vector. Examples of vectors include, but are not limited to lentiviruses, adenoviral, and adeno-associated viruses. The type of vector can also be selected for targeting a specific cell type.

The vectors disclosed herein can comprise one or more promoters or regulatory elements or the like. In an aspect, a vector comprises one or more polymerase (pol) promoters, one or more pol II promoters, one or more pol III promoters, or combinations thereof. Examples of pol II promoters include, but are not limited to the retroviral Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter (optionally with the RSV enhancer), the cytomegalovirus (CMV) promoter (optionally with the CMV enhancer), the SV40 promoter, the dihydrofolate reductase promoter, the R-actin promoter, the phospho glycerol kinase (PGK) promoter, and the EF1α promoter. In some aspects, pol II promoters can be engineered to confer tissue specific and inducible regulation of gRNAs. Examples of pol III promoters include, but are not limited to, U6 and H1 promoters. In an aspect, any pol III promoter can be used. In an aspect, the promoter can be a U6 promoter. In an aspect, the promoter operably linked to the gRNA can be a pol III promoter, human u6, mouse U6, H1, or 7SK.

In some aspects, the compositions described herein (e.g., CRISPR-Cas systems, vectors) can comprise one or more promoters or regulatory elements. In the instance of two or more promoters or regulatory elements, said promoters or regulatory elements can be referred to as a first promoter, a second promoter and so on.

The vector or vector systems disclosed herein can comprise one or more vectors. Vectors can be designed for expression of CRISPR transcripts (e.g., nucleic acid transcripts, proteins, or enzymes) in prokaryotic or eukaryotic cells. CRISPR transcripts, for example, can be expressed in bacterial cells (e.g., Escherichia coli), insect cells (using baculovirus expression vectors), yeast cells, or mammalian cells. Alternatively, the recombinant expression vector can be transcribed and translated in vitro, for example, using T7 promoter regulatory sequences and T7 polymerase.

Vectors can be introduced in a prokaryote, amplified and then the amplified vector can be introduced into a eukaryotic cell. The vector can also be introduced in a prokaryote, amplified and serve as an intermediate vector to produce a vector that can be introduced into a eukaryotic cell (e.g., amplifying a plasmid as part of a viral vector packaging system). A prokaryote can be used to amplify copies of a vector and express one or more nucleic acids to provide a source of one or more proteins for delivery to a host cell or host organism. Expression of proteins in prokaryotes is often carried out in Escherichia co/i with vectors containing constitutive or inducible promoters directing the expression of either fusion or non-fusion proteins. Vectors can also be a yeast expression vector (e.g., Saccharomyces cerevisiae).

In some aspects, the vector can be capable of driving expression of one or more sequences in mammalian cells using a mammalian expression vector. Examples of mammalian expression vectors include but are not limited to pCDM8 and pMT2PC. In mammalian cells, regulatory elements control the expression of the vector. Examples of promoters are those derived from polyoma, adenovirus 2, cytomegalovirus, simian virus 40, and others disclosed herein and known in the art.

In some aspects, the regulatory element can be operably linked to one or more elements of a CRISPR system to drive expression of the one or more elements of the CRISPR system. CRISPRs are a family of DNA loci that are generally specific to a particular species (e.g., bacterial species). The CRISPR locus comprises a distinct class of interspersed short sequence repeats (SSRs) that were identified in E. co/i, and associated genes. The repeats can be short and occur in clusters that are regularly spaced by unique intervening sequences with a constant length.

As used herein, “CRISPR system” and “CRISPR-Cas system” refers to transcripts and other elements involved in the expression of or directing the activity of CRISPR-associated (“Cas”) genes, including sequences encoding a Cas gene, a guide sequence (also referred to as a “spacer” in the context of an endogenous CRISPR system; e.g. guide RNA or gRNA), or other sequences and transcripts from a CRISPR locus. In some aspects, one or more elements of a CRISPR system can be derived from a type I, type II, or type III CRISPR system. In some aspects, one or more elements of a CRISPR system are derived from a particular organism comprising an endogenous CRISPR system, such as Streptococcus pyogenes. In some aspects, one or more elements of a CRISPR system are derived from Staphylococcus aureus. Generally, a CRISPR system can be characterized by elements that promote the formation of a CRISPR complex at the site of a target sequence (also referred to as a protospacer adjacent motif (PAM) in the context of an endogenous CRISPR system).

As used herein, the term “target sequence” refers to a sequence to which a guide sequence (e.g. gRNA) is designed to have complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. Full complementarity is not necessarily required, provided there is sufficient complementarity to cause hybridization and promote formation of a CRISPR complex. A target sequence can comprise any polynucleotide, such as DNA or RNA polynucleotides. In some aspects, a target sequence can be located in the nucleus or cytoplasm of a cell. In some aspects, the target sequence can be within an organelle of a eukaryotic cell (e.g., mitochondrion). A sequence or template that can be used for recombination into the targeted locus comprising the target sequences is referred to as an “editing template” or “editing polynucleotide” or “editing sequence.” Disclosed herein are target sequences. In an aspect, the target sequence(s) can be selected from one or more of the sequences listed in Table 1. In an aspect, the target can be MSUT2 (also known as ZC3H14). The mouse MSUT2 gene ID is 75553. The human MSUT2 gene ID is 79882.

The mouse longest coding mRNA → protein is: NM_029334.2 → NP_083610.2 (SEQ ID NO: 26) 1 ggggacgcgc acggcggagg cggagcggcg goggcagogg cggcagcggc agcggcagcg 61 gogtaggggg cccaggctgc agggtggcag cccgcggcgg gctccaggta accgaggcgc 121 cgcgcagtgc cgagcoggcc gcccgccgcc gagccatgga aatcggcacc gagatcagcc 181 gcaagatccg gagtgccatt aaggggaaat tacaagaatt aggagcttac gtagatgaag 241 aacttcctga ttacattatg gtgatggtgg ccaacaagaa aagtcaggac caaatgacag 301 aggacctgtc cctgtttcta gggaacaaca caattcgatt caccgtatgg ctccatggtg 361 tattagataa actgcgctct gtcacgactg agccctctag tctaaagtct cctgacgcca 421 gcatcttcga tagtcacgtg ccttcaaaca agagcagttt cagtcgggga gatgagagaa 481 ggcacgaagc tgccgtccct ccccttgctg tttctagttc tagacctgaa aagagggatt 541 ccagagtttc tacaagttca caggagcaga aatccactaa tgtcagacat tcatatgatg 601 atggagcttc cacccggcta atgtcaacag tgaaacctct gagggaacca gcaccctctg 661 aagatgtgat tgatatcaag ccagaaccag atgatctcat tgatgaagac ctcaattttg 721 tgcaggagaa tcccttatct cagaaaaaac ctacagtgac acttacatac ggttcttctc 781 gcccttctat tgaaatttat cgaccacctg caagtagaaa tgcagacact ggtactcact 841 taaacaggct gcaacttcat ccgcagcaaa gcagtgctca cgctgccaag cagctggatg 901 tacaaagcag ccaggtatcc gaagcaggac ggttgtgtga gccaccagtg cttagcagcg 961 tagaagacac ttatagcccc ttcttcagaa acaacttgga taaaatgagt attgaggacg 1021 aaaactttcg aaagagaaaa ttgcctgtgg taagttcggt tgttaaagta aaaagattta 1081 gccatgatgg agaagaggag gaagaagatg aggattatgg gacccgcata ggaagcttgt 1141 ccagcagogt gtcagtacca gcaaagcctg agaggagacc ttctcttcca ccttctaaac 1201 aagctaacaa gaatctaatt ttgaaggcta tctctgaagc tcaagagtct gtaacaaaga 1261 caactaacta ttctgcagtt ccacagaaac agacacttcc agttgctccc agaactcgaa 1321 cttctcaaga agaattgcta gcagaaatgg tccaggggca aaacagggcc cccagaataa 1381 gtccccctgt taaagaagag gaagcaaaag gagataatac aggaaaaagt caaggaactc 1441 aacagaggca attgttatcc cgactgcaaa ttgatccagt aatggtagaa acaatggaga 1501 tgagtcaaga ttactatgac atggaatcca tggtccatgc agacacaaga tcatttattc 1561 tgaagaagcc aaagctgtct gaggaaatag tagtgacacc caaccaggat tcggggatga 1621 agactgcaga tgcccttcgg gtcctttcag gacaccttat gcagacacga gatcttgtac 1681 aaccagataa acctgcaagt cccaagttta tagtgacgct ggatggtgtc cccagccccc 1741 caggatacat gtcagatcaa gaggaggaga tgtgctttga aggaatgaaa cccgtaaacc 1801 aaacttcagc ctcaaacaag ggactcagag gtctcctcca cccacagcag ttgcatttgc 1861 tgagcaggca gcttgaggac ccagatggta gcttttccaa cgccgagatg actgacctga 1921 gtgtggcaca gaaaccagaa aaacttctgg agcgctgcaa gtactggcct gcctgtaaaa 1981 atggggatga gtgtgtatac catcatccca tttcaccttg caaagccttt cccaactgta 2041 aatttgctga gaaatgtttg tttgtgcatc caaattgtaa atatgacaca aagtgtacta 2101 aagcagattg tcccttcact cacatgagta gaagagcctc gatactgact ccaaaaccag 2161 tgtcgtcacc agcaccgtct tctaatggcc agctctgccg ttacttccct gcttgtaaga 2221 aaatggaatg tcccttctac cacccaaaac actgtaggtt taacactcag tgtacgagac 2281 ctgactgcac attttatcac cccaccatta ctgtgccacc aagacacgcc ttgaaatgga 2341 ttcgacctca gagcagtgag tgatgcccta gtcctacctg gcagaagatc atgcagtttg 2401 aaagcttcca tcttctgatg agagatgttc tacagaactt gtcacgtctt tgaaatttag 2461 aatatattgc tttcataata cgaattttac tgccccactg aagtgtctaa tttttcaagt 2521 ttgtaagttt attaagtggt ttcaacattt tttgtttgtt cgttttgact atgaaaaaga 2581 cagtttaaag aaaagccaaa ttctattaaa acatttgcgg catgtttgta cattgctgtt 2641 taatatcatt tttggtaatg gtacttgcag cttagggctg tagtgctgtg ggaaggccag 2701 tgtcctcaga gctgaagcac ttttcagctt ttcccaaagg taatgcagtg tctgtaaccc 2761 agcgtggtaa cagtggccag gctttgaaac tgaggcagct ttggaacaac tagtttaaat 2821 ttcttttttt agtgtctaaa tgaatttgct ctgagaagca taatgcagac tttattttga 2881 gtgctacttt ggtagagtgg accgaggtcc tgtgcctttc tgaaagtgag cagagacatg 2941 gtcataaagg gtaagcatag ttggaatgac gatgtaaaaa tatatggaca gttctttgga 3001 atgctcccat ttactattag cttatcattt tataagtaat tttggaggga ctacattatc 3061 acaaaagtat acaaaaattt ttacaggcat atgtacagaa agtatcagaa aacagacttt 3121 gaactcacaa gaatataaat atacgtatat attcccatat tctgaaaaat atcatcagaa 3181 ataaccccac agaaaatata cttatgttat tactaaagat cattcttgaa atgtagaagt 3241 tgagatttaa gtggtatatt ttaaatgaca gaactatatt gcagagatag gaaggtaaac 3301 ttgacaatag gatgaaactt ggcctactgt actatggagt tttatgtgtg gtttttgaaa 3361 ctgttaaggc aagatgtgtc atgttttaga actaaataac agacaactga tttcaaaaac 3421 gtgttgtttt aaaaattaaa gtgtaaacgg tggttagcaa aggggataat aaaagctcaa 3481 acattttgag gaccaaattt aactgttaag atacaataaa gtcacatcta taaaagtctg 3541 tgtttaataa tgtgaa. The human longest coding mRNA → protien is: NM_024824.51 → NP_079100.2 (SEQ ID NO: 27) 1 ggaggcggtg gtgtcccggc tgcggggtag gagtccgcgg cagcctccgg gtaagccaag 61 cgccgcgcag tgctgagttc ccgcacgccg cagagccatg gagatcggca ccgagatcag 121 ccgcaagatc cggagtgcca ttaaggggaa attacaagaa ttaggagctt atgttgatga 181 agaacttcct gattacatta tggtgatggt ggccaacaag aaaagtcagg accaaatgac 241 agaggatctg tccctgtttc tagggaacaa cacaattcga ttcaccgtat ggcttcatgg 301 tgtattagat aaacttcgct ctgttacaac tgaaccctct agtctgaagt cttctgatac 361 caacatcttt gatagtaacg tgccttcaaa caagagcaat ttcagtcggg gagatgagag 421 gaggcatgaa gctgcagtgc caccacttgc cattcctagc gcgagacctg aaaaaagaga 481 ttccagagtt tctacaagtt cgcaggagtc aaaaaccaca aatgtcagac agacttacga 541 tgatggagct gcaacccgac taatgtcaac agtgaaacct ttgagggagc cagcaccctc 601 tgaagatgtg attgatatta agccagaacc agatgatctc attgacgaag acctcaactt 661 tgtgcaggag aatcccttat ctcagaaaaa acctacagtg acacttacat atggttcttc 721 tcgcccttct attgaaattt atcgaccacc tgcaagtaga aatgcagata gtggtgttca 781 tttaaacagg ttgcaatttc aacagcagca gaatagtatt catgctgcca agcagcttga 841 tatgcagagt agttgggtat atgaaacagg acgtttgtgt gaaccagagg tgcttaacag 901 cttagaagaa acgtatagtc cgttctttag aaacaactcg gagaaaatga gtatggagga 961 tgaaaacttt cggaagagaa agttgcctgt ggtaagttca gttgttaaag taaaaaaatt 1021 caatcatgat ggagaagagg aggaagaaga tgatgattac gggtctcgaa caggaagcat 1081 ctccagcagt gtgtctgtgc ctgcaaagcc tgaaaggaga ccttctcttc caccttctaa 1141 acaagctaac aagaatctga ttttgaaggc tatatctgaa gctcaagaat ccgtaacaaa 1201 aacaactaac tactctacag ttccacagaa acagacactt ccagttgctc ccagaactcg 1261 aacttctcaa gaagaattgc tagcagaagt ggtccaggga caaagtagga cccccagaat 1321 aagtcccccc attaaagaag aggaaacaaa aggagattct gtagaaaaaa atcaaggaac 1381 tcaacagagg caattattat cccgactgca aatcgaccca gtaatggcag aaactctgca 1441 gatgagtcaa gattactatg acatggaatc catggtccat gcagacacaa gatcatttat 1501 tctgaagaag ccaaagctgt ctgaggaagt agtagtggca ccaaaccaag agtcggggat 1561 gaagactgca gattcccttc gggtactttc aggacacctt atgcagacac gagatcttgt 1621 acaaccagat aaacctgcaa gtcccaagtt tatagtgacg ctggatggtg tccccagccc 1681 cccaggatac atgtcagatc aagaggagga catgtgcttt gaaggaatga aacccgtaaa 1741 ccaaactgca gcctcaaaca agggactcag aggtctcctc cacccacagc agttgcactt 1801 gctgagcagg cagcttgagg acccaaatgg tagcttttct aacgctgaga tgagtgaact 1861 gagtgtggca cagaaaccag aaaaactttt ggagcgctgc aagtactggc ctgcttgtaa 1921 aaatggggat gagtgtgcct accatcaccc catctcaccc tgcaaagcct tccccaattg 1981 taaatttgct gaaaaatgtt tgtttgttca cccaaattgt aaatatgatg caaagtgtac 2041 taaaccagat tgtcccttca ctcatgtgag tagaagaatt ccagtactgt ctccaaaacc 2101 agcagttgca ccaccagcac caccttccag tagtcagctc tgccgttact tccctgcttg 2161 taagaagatg gaatgtccct tctatcatcc aaaacattgt aggtttaaca ctcaatgtac 2221 aagaccggac tgcacattct accatcccac cattaatgtc ccaccacgac atgccttgaa 2281 atggattcga cctcaaacca gcgaatagca cccagtcctg cctggcagaa gatcatgcag 2341 tttggaagtt ttcatgtact gatgaaagat actctacaga acttgtcaaa tctttgaaac 2401 ttggaatata ttgctttcat aatatgaagt tttattgcct atctatctga agtgtctaat 2461 ttttcaagtt tgtaagttta ttatgtggtt ttaacattgg gtgtttttgt tttgttttta 2521 ctatgaaaag acagcttaag gaagagctaa attctgttaa aatatttggg gcatgtttgt 2581 gcactgctgt tgtgaggatc agcatatgaa attgacatca tggttagtca tggtactgca 2641 gcttaggggg ctacacggtt gctgtgtgag tggagagatg cagtgaggca gttgtcatta 2701 ttctaaaaat tgtactactt tcacttttcc caaagattat ataatgttca taatccacca 2761 tgaaaacagc attggccaaa ggtactgagg ctgcttaaaa tattcaattc tgctttttaa 2821 tttttaagtg aatttagttt gaaaagcatg attatacagg cctctcaggc tgagtgctac 2881 tttggtaaag ttcccagttt tcctgccttc tgtgacagga tgaatgaggt gggtatggac 2941 agtggaggca gctggaatgg caagtgcaga aaataggaac agttctatac agtgctctca 3001 tttactaata acataatgcc ttctaaataa tttttttggg aaactacatt atcacaaaat 3061 tatacaaatt tttttacaag tatttacata ctgtatctga aaacagactt taaagtcaca 3121 agattataaa tgtacatata tattctcaca ttctgaaaaa taacattctc agaatccaca 3181 gaaaatatac ttagttacta ctgaagataa tttttgaaat gtaaaaatta gatttaaata 3241 gtatatttta aatgacagaa ctataattac agagatcaga tcagataggt aaactgcaag 3301 atagatagga tgaaactttt ggcctactgt attacttaca gagttttttt gtgtgtggtt 3361 tttaaaactg ttaaggcaag aagtgtcaaa tgctttagag ttaaataaca gatcactgat 3421 ttcaaagact tggtgtatag tgttaaaaat taaagcttaa aaggtggtta gaaaagtgga 3481 ttaatgcaaa aggggtaata aagactgcaa cattctcagg accaaattaa actgctaaaa 3541 aaaaaaaaaa agttcattga cttgcttagt cgtatactca aatgatgata aacctacatg 3601 tgcaaaggct cacgtttaag attgtcaagc cagcagtcta ctgttgtgtt gccattgctt 3661 ttccattggg agaagaaaga attaaccagt cattaaacca tttggtaagt tgcactttgc 3721 tgtgctgatc ccacaggaaa ggcttgaaac acgagaagca gcaaagacag agcacacaag 3781 tgcataaggc tgttgtcttc ggcttgggtg aaatgacagt tcctcttcat tctaaaggtt 3841 tactccattg aatttaaggc atttgttcat tccagtgttg agatgctttg catctctgca 3901 gaagaaattt attttaaatt gtttaaatat ctggaaatac ttttagctat catttataaa 3961 gatagttttg ttctcagttt cactataaat tatagaacaa atgggaaaca agggtttaat 4021 ttagttcagc cattttacaa ggaaataata aaatactaaa atctgattgt tttttgctat 4081 ttaatagcca ctgcccagac acatatttaa gagtttaatc tttcagttgc tatggcttat 4141 gaacaagcta aggttgacca taaaacattt gttggatgac gtggtttaaa atgatcacca 4201 caaaaaggga ccacaaaaaa aggaaggaaa tgagcatggt tggcgattgg aagcaagggt 4261 accagagggc acagtgtgct ttggcatgca ttttatacat aaaatgaatg gaacaaaagg 4321 tgccagaagt cccaggttac acaatcagga gcttagatac tgcacacaaa aataattatc 4381 tgggttaaaa aagtaaacat agggcagatt ctatatggcc tatcatgttt cttcaccttc 4441 ccctcgttgc tggctgatac agcgaggtgg tcagctgatg actacttagt caatatgacc 4501 tttagtcgtg aaactgacag cagcagtgat taaggctgac ttaatcaggt tggccacttt 4561 gaaggacaga aatgcagtgg aaacagtttt attctatgta gtttacatgc ttaaggttac 4621 agagtttcta cctgcactgt aatggaaata taatttctct gtagccaaaa gctggcaaac 4681 ttgacccaga gggaaaattt aaaactgcag caggctcaaa tgtagagtat ttttcttttt 4741 atgggcaggt tgttcaggga tttttttcct cctttaattt attgactgac tgtaaataca 4801 tgagtagaaa cttaatagtc atgtatttca aaatttggct taatttagga gaatccactg 4861 atgaacaagt accaacttac gtttcaagct tcttagcccc ataatcagtc cttcagccac 4921 agctatttag agctttaaaa ctaccaggtt caatcactgg ttatgctttc tgtgatgtaa 4981 tttagtcatt tctattttta gtattaacca agtattagac acagaaaata ggtattaaga 5041 atcttcatat atcctgtcag accaaatggg attccaggaa cctaaagcga tctattatgc 5101 tataaagata attaacacat taaaaactca tagggtcaat acagcatctt aaacctcaca 5161 cttagaaaaa tatattttta aatagcagtc tacataattt tcaatcttca ggaaactaca 5221 gataggctag acagcgaatt cctgaatgat gagtagtgat ctttggcagc atttaaagtg 5281 aaaagaaata aggatctaag aattcagccc taatccacta aaaaaaggaa ttctaactga 5341 caagttttta caaatggagt tgggctcatt cattttggaa ataaacctat ggagtggcac 5401 acatctaaac aaattttccc aatagaaaaa aggctataaa aattttattc caagagtgat 5461 taaattgtat aatgttgtat atgtgaattt aacacttttg tttacatgtt aaacaaatgt 5521 gtatatatta gactacatta aatatgcaat tctttcttcc agttaaatac tgttgctccc 5581 taaaaccctt acattgtaca ccattgggaa tgattgttca tcatactact tttccattag 5641 tgaggctaca gttatgtttt aaatgtgcga ttacagagat ggcatctgaa cataaactga 5701 tggctcgaaa atgaaaatgg aaatgtagca gccatatact gctaactttg gatctgttcc 5761 tgaattcaaa actactagga gaaaagtgtc ctttataaaa aaggacctta ttaatgccta 5821 aaaaacatca tattctctag gaaagcttgt gtctgtttcc ttagggaaaa tgtttgcctt 5881 ttaaaaactg tgatccttta ggatgatcat gactttccct ttccttatgg aaatgcaaga 5941 ataaaatatt tcattaaaca atgaaccttg aaaataaaat ataaacatta agaaaccatt 6001 ttgctaaaaa gataatgaaa attatccaaa ttgggttttt gagttcttct gtaaagagtg 6061 ctctacccta aattttccca gcaggtctgc cgaaatcaca cacttcccaa tacaggggga 6121 cttggccttt accatcaagt attcgatcct tccttgaaat ggcattatct ggcagtgtat 6181 ggattacgga ttatacccag tgcatatagc aaatattttg aacagatcag tctttcacta 6241 ttttgatgat tctgggcatt tctccctgtt acagtcttgg gttagcacca cttgaccatg 6301 cagggttggg ttttggtttt tcttctctgt aattctggtc tcaaagttaa tttctgtagt 6361 catctcagca tctctcagtg aggtgtatgt acacatttcc agacaaataa gctgcaatca 6421 gagaagaaaa ttgcagggag ttaattatgt ttttagattt tcataacagt ttaatatttt 6481 tcagttgtgc tttcaggtta catgtgtaat atttttcctc tttaactcct tttattctgt 6541 atttgcataa atatgagatt ctgaagagcc atctggttat actaccttct actaatgttg 6601 actagctgat ttcataaacc aaagctgtag gagttgttgt attaagtctc ttaactagta 6661 acatagtctg ctcttcatgg gctgagaaag ttactaacct gcagtcatca cctccagcac 6721 taacaacatg tcgatcacca ctggtaaatc gaatatttgt cacatggggc gaatgaccca 6781 agaacctttt gtgttttgcc taaaaaacaa tgacagacaa gctcagggca tttggtgcac 6841 acagaagtca aaggctctta ttaggaacta taatctctat gacaagagct gtggagagag 6901 tagggagtta gcaccgcagc cagtgattag aatgcttttc agcatgagta gtggatctgc 6961 aaaaccaggc tgtgtgggca gtcagatgtc tccaggtact ctgaccattt ttctctaagg 7021 aaaagcattt gaaatttgat aactgattat aggtttggtg aaaagctaat tacagctttt 7081 gtaggatggt tccaaagatg gtattactcg agggagagga tttgtttcta atagctttta 7141 tttcaaagta aatagattta gaaagtttgg ggaaaaattt agaaattagg acaaaacatt 7201 ttaaatatat ggggaaaagt gctgatgata agacatcaaa attaggagta aactgataat 7261 agtaaacaaa acacaaactt acaaattttt ctggacatgg gaagtcaaat aacttaacca 7321 tgccaaagtc atctcctgta acaagactga ttcctgaatg agatacacag gcacagttga 7381 catcagcttt ctcagcatgt ctggaccaga ttcccaaaac ctcatctcct agaatactag 7441 agggaaggaa caaaagaaaa ctcatcatgg caagtgcggg caggttgact atattcaaaa 7501 agtttcttgg caattaatct ctaagtaccc tatcatgtta cttaaaatac aggaagtaaa 7561 ttatggtaag ttgtttggag acctgaattt catcaggata tcaactcctg ccttttaaaa 7621 atgacatttt ataatttgaa gggtttctag attaatcttt ttaagattaa agtagtactt 7681 tatgaaaact gatagaacta ttttttcttt tttttttttt gagacggagt tttcgctctt 7741 gttacccagg ctggagtgca atggcatgat ctcggctcac cgcaacctct gcctcctggg 7801 ttcaagcaat tctcctgcct cagcctcccg agtagctggg atcacaggca tgcgctaaca 7861 tgcccggctt attttgtatt tttagtagag acagggtttc tccatgttgg tcaggctagt 7921 ctcgaactcc cgacctcagg tgatcacccc cgctcggcct cccaaagtgc tgggattaca 7981 ggctgagcca ccgcgcctga ctgaaaactg atagaactat ttttcaaatt aaaagtgcta 8041 cttggctggg tccagcagca cataccagta atcccaacat tttgggaggc tgaggcagga 8101 ggactgcttg aggccaagag tttgagacca gcctgggcaa tattgtgaga tccctatctc 8161 tacaaaaata aaaatgactt atgacatagg aattaaaaaa atttcagaga tggggtcttg 8221 ctatgttgcc caggctggta tcaaaacttc taggctcaag tgatcctccc acctcggcct 8281 gctacatcag agattacagg catgagccac tatatgcctg gctgatacag gaatttgatg 8341 gcatttttca ttggccaaaa aaatggatag tcatggttac ctgtcataca gccaggaaat 8401 ttgaacaaat ttggaagctt tgacttctaa tagattcaag atagcattcc tttagataga 8461 gaattaataa cagttgctta acagcaccca ataccttttt gccagtcatt aaatttagca 8521 ttaagaaaaa tatcagggta tctttaaagt taaaactttg atttccttaa aaaaaaaact 8581 tgataaatca tggaaactga taaaacatgg aaatatattc aataaaaagg ggtcccaaca 8641 tgaacatacc atttcaaaat atggtaacaa aaacttgaaa ctcaattact attccttatt 8701 ggaatggctc taacagttca gaaataggat tttctaactg gccttcaaag tcagttcttg 8761 ccttgtgaat atataagtat ttacctagtc catgtagccc aagtaattct gtcaatagcg 8821 gcatgatcca taagatgttt tcctgaaggc acttcataga catgccgttt atagcagcca 8881 ctagagacct ttttcatcag attaaaatgg gacaagaatt ccattaggtg agagacaaaa 8941 tccacagggg gtttacagaa tactagcata ttgctacttg atttacatgt ctaacattat 9001 taagtatgca aaagatcact acaaaaactt aataggagaa aagctctgat aagtggggga 9061 ggaaagggga gctgtaggtc agaaggtaca aagggaggag ttgagaagct ggagctctgg 9121 agctcaggaa ctttaaatgc attcactaac acgaaatgta aaagcagaag aacttgccac 9181 ctgggtatac agtattggta ctgtacctgg agataactgc tatctgcaga gaagtccatt 9241 tgaatgacaa agcttggaat gtctttgcag tagctgattc tgttaagagt ggggcccagc 9301 gttaggtcat aaaaatccac tgagttctca ctagaaccta ctgccagata ccgggaatcc 9361 ggactaaatc tgaatcaaaa caaaacgtaa aaagtattag accacatgaa gtattataaa 9421 tacttaagat cagtgacttt tcctttctag ttcttaaaag taacgtgtga taaggcctca 9481 aatagattta cctgtcagac acaactgatc atgtatactg agattgtctg ggttacatga 9541 aataaggaag ctttatattt tacttaaatt ttaaatattt ccccaattgt catctcccaa 9601 ttcctttaaa aacgtctaat ggcttaaaaa aactttctta ggccaggccc agtggctcac 9661 acctataatc ccagaacttt gggaagcgga ggcgggcaga tcacctgagg tcgagagttt 9721 gagaccagcc tgaccaacat agagaaaccc tgtctctact aaaaatacaa aattagccag 9781 gcatggtggt gcacgcctgt aatcccatct actcgggagg ctgaagcagg agaatcgctt 9841 gaacccagga ggcacaggtt gtggtgagct gagattgcac cattgcactt cagcatgggc 9901 aacaagagca aaactccaac tcaaaacaaa acaaaacaaa atttaatttt ttaaatagag 9961 gcggggtctc actatggtcc caaactcctg gcctcaagca atccttcccc cttggcctcc 10021 caaggtactg ggattacagg tgtgagccac aacacccagt cagaacatct cagcttttaa 10081 aagccattag cattacataa ttaataagct aacaattcat taagatagtt ttcttccatc 10141 tggaaaaaac gttgtcttaa tattaagcaa agaacacagc ccagcttaac taacctccag 10201 ttattaaggt gaaatgacac aacttgaatc ttggaagaag aatttttttt ttttgagacg 10261 aagtctcgct cttgtctccc aggctggagt gcgatggcgc aacctccgcc tcccgggttc 10321 aagcgattct cctgtttcag ccccctgagt agctgggatt acaggcgcct gccaccacgc 10381 coggctgatt tttgtatttt tagttgagat ggggtttcac tatgttggcc aggctggtcg 10441 agtactcctg acttcaggtg atctgcctgc ctcggcctcc caaagtgctg ggattacagg 10501 catgagccac cgcgcccggc ctgaagaact tatttaaaag acaaagtgaa atgctatttg 10561 cctagcaatc tttggagtca tatgggacaa ttcagtctct tgaaatggcc catgagtctt 10621 actgaggtac gatagagaca tgtaaaagct aagggaagcc actgttacta ttttatatat 10681 tgaagttctg aggaaggttt catttgtaaa aggattttac tgatgaaaag tgtacaagct 10741 tttgacagac ctagattcaa taatcttatc tactgatcac acggaagtac tccgtaaatg 10801 gtagccactg ttgaaaaatg cttaagcact gaaaaacaaa ggtttaagaa acatttaaat 10861 taatttggat tctggaacat ttaatcaata ggtattgatt aaattaatga actacatatt 10921 cccaaactga ggttactaag agaagatatg tttgaaatca caactttagt tttccagggt 10981 gacaactttt gaagggcaga tagctctctt gtattacagt gggagatacc tcttggtggg 11041 atgaacttaa tggacatggc taagtgttaa catgaattca tcaaacatta cctactagta 11101 cttgctatta tagttggtgc ccagtgggtt tataatttag caagaagaat taagtagtat 11161 acaaacagcc atattttagc atacaattta taatacggga aatgctacag gccctgggga 11221 cctctttttg aaggcaaggc tatggaaaat tttacaaatg gaagttaaat caagtatata 11281 ctagaaactc tattccattt gttcactaac ctgatatcat ggattgcaca tctcctgtct 11341 ctcttctttc cccatatttt tagagaactc actagtaaaa tgataaattc tccatttttc 11401 attccaatag ccaccatgtc cccttcaggg ctgtaacaca cagtacgagc agcatgtccc 11461 aaattcactt tgtttaacat cttctgcatt taaaaaaaaa aaaaaaaaga gtcataggaa 11521 acattaagtg aagtacttct aaattatacc agtttcccct caaaatgctc aacagaattc 11581 tggcagttct ttaagtacta gcaatttaga acttccaact tttcttttta gaagttgtaa 11641 cctcttttaa aaaaattatc tgtacttact ttatcagcaa tatcccaaag tctcactgtc 11701 ccatcttctg cagcagaaag gaaaaaatcc ctggaaggat gtgttgctag tccccagatt 11761 ggcccatcca catgaccgtt aactaaaata ttacaagctg catttttctc tccaacttcg 11821 attatttcag cattccttgt cccaacaagg atcttgccct gaaacacaag caggaccaat 11881 acagtgaatg taatacaaca gctgcttttc ttcttcataa tataaaaatg accctattga 11941 cctgctttca gagaactttt tgctttgagc taatctagta gcaaggcagt cattagctca 12001 tgcaaatttt tctatgacta caggcacaca tctatctgta agcacaatgg gctagattac 12061 atattagagt ccatgctaca gaatagaact tttctgtggc agtacacctg gattcttcaa 12121 taatcaaagt ttttatttga taatcttagg atttccaaac tggggtcagt gcagtgggat 12181 ataggaaaaa ataatagaat ttatttttta gttaaaaagt aaaagcttaa ctacaattta 12241 atatgcaggc tgaagataat atccgtatga tttataaata cacttaataa gtacaaacac 12301 gctcaaaaat tttcatagga gttgtagttt tgaattttta ttttgaaatt gacacataat 12361 tatacatatc tatagggcat agggtaatac gcataaccat cacctcagac atttatcatt 12421 tctttgtgat ggaaactttc aaaatcctct cttgtaaata cctgaaaata cataaatacg 12481 tgattcttaa ctatagtcat cctacagtac tacagaatac taaaacatac tattcctatc 12541 tggctgtgta aacttgtatc ctttaaccag tccttcccta tccccctccc cctccccctt 12601 gtccgcctcc agtaaccact attctactct ccacctctgt gggatcaact tttttagttt 12661 ctgcacagga gtgagaacat gtatttatct ttctgtgcct ggcttatttc acttcacatc 12721 atgtcctcca gtctcatcca tgttgccacc aagaatgaca gaatttcatt attttttatg 12781 gctgagtagt atttcattgt ttgtttactg cacgttttat ctagggaatg tgtgtttttt 12841 taaaaaatgg agacagctgt cctaatatga gtcaactgcc aagggctttc aattatgtct 12901 actagagttg ttaaattggc agattctaga aaatattgga ggtttacata cagtatttag 12961 acagaatagc ttcctagctt atgcaccaca ctggtgctaa ctttggcaaa gaaagcagca 13021 aagacagagt aatgttggca agcaaatcca tcgttatgca ttattaagta ttgttcatta 13081 ggctgcaaag ggtgagggaa tcacagtaat aaccactttc tgttttctgc tgcactgtat 13141 cagctcatgg aacatcttac tttgcctctg cacacagaac gaacacaatc tgtggcttgt 13201 cctgtctcaa gcctgaaggc acggcaccgc ctcagttcct gatcccacag tttaaccgct 13261 cctccttctt ttgacctaag taaataacca agccagagta agtgttcatt attggctact 13321 ataattttta ttataaacaa ataccaagtt ataagcagaa tctttttttt ttaaaaaggc 13381 cctgatattt ataatttacc tctaatattc ttgtaaactt tctatggcaa tttgaggata 13441 tactatatct cagtcaaaat aaacatccag tttcagtgaa ttttattttg agaaatactc 13501 tttttttctg acatgagcat aattttattt agcctctaca atacattaca atacattatc 13561 ctctctcata atactttttt tttttttttt aagatgtagt ctcgctctgt ctcccaggct 13621 tgagtgcagt ggcatgatct aggcttattg caacctctgc ctcccaggtt caagcgattc 13681 tcctacctca gcctcccgag tagctagcat tacaggtgtg caccaccaca cccagctaat 13741 ttctgtattt ttagtagaga tggggtttca ccatgttggc caggctggtc tcaaatacct 13801 tgacctcagg tgatctgcct gcctcggcct cccaaagtgc tgggattcca ggtatgagcc 13861 actgtgcctg gcctcataat acttcttgat taggaagatg taaaaaaaca attttattaa 13921 aaggataatg gaaatgtaag gcaaaataat agaattacaa atgctatgct acagagttga 13981 tttatttatt tttttgagac agagtgtcgc tctgtcacct ggcctggagt gcagtggtgt 14041 gatctcggct cactgcaacc tgtgcctccc aggttcaagc gattcttctc cttcagcctc 14101 ccaagtagct gggattacag gcaccatgcc tggctaattt ttgtattttt agtagagatg 14161 gagtttcacc atattggcca ggctgatccc aaactcctga cctcgtgatc cgcccacctc 14221 ggcctcccaa agtgttggga ttacaggcgt gagccactgc aactggccca gagcttattt 14281 ttgaaggcca aaacagaagc atatttattc cctatcaggt gttaaaatat ctcactggaa 14341 cagtttagca ggcttctagt gagtgggggt gtgcaggagt aaatgacgtg ggaaatacaa 14401 gtgttggagg acgaaataga gcccatttat ggattttatt cctggaaggg ctgaaaaatg 14461 tattccttcc ttttctgcta gatgaattgc ttgtctgaaa gcatgcctat gtgcattctt 14521 cctttatgta aaaggcacaa attctgcgct tgtgtttaat taacatatgt gggttctttc 14581 aatcctgtat tgaaatgtac ttcttagtca actatatgtc acattttttt ttgtttttgt 14641 ttttgttttt taaatggggt ctcactctgt cacccaggct ggagtgcagt ggcaccatca 14701 cagctcacta aagccttgac ctccccaggc tcaagtgatc ctcccacctc agcctcctga 14761 gtagcaggga ctacaggcat gtgccaccac acccggctaa ttgttgtttt ttatagcgat 14821 ggggtttcac catgttgccc aggctggtct tgaactcctg ggctcaagcg atccacctgc 14881 ctcagcctcc caaagtgata agattacagg tgtgagccac tgtgcctggc ctacatgtca 14941 tgtttcaaca tgcatatgac tatgttggtg acaaatcaaa tcataagtat ctggttactg 15001 ttgggagatt tgaaaatcac tcagaagaga cctcttctca aattttgagg tcttgtataa 15061 aacagtttaa atttgcctca agcaaaagga aacaaggcag ttctctctag ttccctcatc 15121 cttttctaaa gcaacaatgt gcattctact ccttagaatc cattctgaac aaaaagagag 15181 caggcagtca aaatacaacc ctggctccag attcccccat gggcctccta ctcagcaaat 15241 catacacagg catacagaca ttaagaaaag taactcaact tgtaggacaa ctacctatcc 15301 acacctcaga aaaagtatca ccccaacatg aaaaaaattg gaagtgaatt aagaccagaa 15361 atgagaatca aatagaaggc acataaaagg taataaagga gaagcatatg aggaggaagg 15421 toggagagga cactctgtgt agcctagaaa caactagaat aattaactgc aaacctcagg 15481 taggtcacaa atgcataaat attctgtgaa aagaaagagg actcacggcc tttcctttcc 15541 cccagtcacg ataagtccat ctcgcagggt ggtgtacatg gcaaacacag gcccgttgtg 15601 agctctcgcc acgattctac acaatatgtg atctttccac acacagacat caccactgat 15661 ggtacctgta aacgtcaagt tattctgaaa aggagtgggg gagggggaga caaactcatc 15721 aaaagttcaa atagagttta aatagataat tttctatgta tgtgtaatgc tgtctcaccc 15781 ttgatacaaa gagcatgcat cgtgtagtgg cagcagcact gaattcacga gtcaggaaac 15841 ctgaacggga ggcttagctt tgtcaggacc ttttcctttc caagtctgtt gcttattagc 15901 tagaataacc ttagacaatt cttcccttcc aattctaaca tactataatt ctagggttta 15961 ttttttattt ttttgagacg gagtttcgct ctttgttgcc caggctggag tgcaatggtg 16021 cgatctcagc tcaccacaac ctctgcttcc caggttcaag tgattctcct gtctcagcct 16081 cccaagtagc tgggattaca agcgccagcc accacgcccg gctaattttt gtatttttag 16141 tagagacaga gtttcacctt gttagccagg ctggtcttga actcctgact tcaggtgatc 16201 ttcccgcctt ggcctcccta agtgctggga ttataggtgt gagccactgt gcccggcctg 16261 agccacggtg cctggcctgg tcttatatta agaataccca aaatgttcaa ctgaaatttg 16321 acatggcaca aacatttcaa tagtcttttt ctcaaaaatg taagtgtact taaatattct 16381 aaaattataa cttttcctat aagtattgca taatcacaaa aacaaaaaat gcacttagtt 16441 tttcgatgca ccaaaggatt tatacagcct agccaatgca ggatattaaa ggaaagagat 16501 gtggattgga agccacaggt ccagatgaga tggaataaag tgagaggaga gcaggtctcc 16561 tgaacaccct tctgtcaggg ccaggaattg tgctatttcc ttctgtctca ctacctcctt 16621 cttccctcga agtagagaca ctggcccaga gcacttccag ctgtatgata agcagtgtgt 16681 taaatgataa aaagcaaagg aaatcctaaa ccctagtacc accttaaatc atttgaaaat 16741 catgtttctt gatttacctt tctctctgac aaatttttag gactatgaag aactactagg 16801 aagacagaaa ttttaggata tttagggtga caattagaag attaaggaag gcttttgagt 16861 ataacagtag tccaaggaat caaatgttca tcagaatcct tattatggtg gctcatgcct 16921 gtaaacccag cactttggga ggtcaagatg ggaggatcac atagcttagg agcttgagac 16981 cacctaggca acatagcgaa accctgtctc tactaaaaat gaaagaaaaa ttagcctagc 17041 atggtggttc ctgccctgta gtcccagcta ctaaggaggc tgaggatcac ttgaacctgg 17101 gagatggagg ctacagtgag ctataatcgc accattgcac cccagcccag gcgacagagt 17161 gagatactgt gtcaaaaaaa aaaaaaaatc cttttccccc tctcattaac attcttttca 17221 ctccctaatt tctgaaagaa ctagattttt gaaagatgaa atatatgctt gaccagggca 17281 tgtaatgatt agcagatcac agtatcatct caacaacatt catgtggctg atgatctaag 17341 gcaagagaat gtaaagtagt caaagtcaca ctatgtgcat tttaagagac atactgcacc 17401 aaatgcaata gcgagcatgg tctgcatccg ggcatcttcc agtgtgctca gtagcccttt 17461 tttgctaaga agagctcttc ctgccagggt ccagaacttc acatgtttta ctcccactga 17521 gacaaactgg gtatctgaat ctggtcggaa ttctgccaca aaaatacgtt gattgtgacc 17581 agctctgctg gcaattttgg cacctgacaa gatacaacaa aattatctag gttattacaa 17641 gaaccaagct aatcaacagc atcaaacaaa tatgtaaaat acatagttca aaaaacaaag 17701 gcttagaaga gaggccaatg gcccctgctc tactacctag caatacatga tttacaatta 17761 tttgtgtatt gagtcctttt cacttatctt cgctccatta acttttcttt atataacgta 17821 aatgttttgt ctaaagtgtg gtaggtaata ttatcctgct gatctgccat tatcattaga 17881 aatatacata attttcataa gaatctccaa aaccaatcaa atcattaata ataaatacat 17941 agtttcttgc tggaagaaaa tagcagtgaa tcatttataa tgctaataat ggtttcatta 18001 atttatctgt tttgtgaggt tacagttcca ctgggctttt aaagtgaaat atacctacag 18061 taccactgtg tacagtatat tgcataggcc tccactgaat gattgtttca accaccaact 18121 ttaagacaaa tattaaatac agaattccta cta.

A guide sequence (e.g. gRNA) can be any polynucleotide sequence having sufficient complementarity with a target polynucleotide sequence to hybridize with the target sequence and direct sequence-specific binding of a CRISPR-Cas system or CRISPR complex to the target sequence. In some aspects, the degree of complementarity between a guide sequence (e.g. gRNA) and its corresponding target sequence is about or more than about 50%, 60%, 70%, 75%, 80%, 85%, 90%, 95%, 99%, or more. In some aspects, a guide sequence can be about more than about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50 or more nucleotides in length or any number in between.

The target polynucleotide of a CRISPR complex can be any polynucleotide endogenous or exogenous to the eukaryotic cell. For example, the target polynucleotide can be a polynucleotide residing in the nucleus of the eukaryotic cell. The target polynucleotide can be a sequence coding a gene product (e.g., a protein) or a non-coding sequence (e.g., a regulatory polynucleotide or a junk DNA). It is believed that the target sequence should be associated with a PAM (protospacer adjacent motif); that is, a short sequence recognized the CRISPR complex. The precise sequence and length requirements for the PAM differ depending on the CRISPR enzyme used, but PAMs are typically 2-5 base pair sequences adjacent the protospacer (that is, the target sequence). A skilled person will be able to identify further PAM sequences for use with a given CRISPR enzyme. In an aspect, the PAM comprises NGG (where N is any nucleotide, (G)uanine, (G)uanine). The target sequence corresponds mammalian suppressor of taupathy 2 (MSUT2). In an aspect, the target sequence can be a MSUT2 gene sequence. In an aspect, the target sequence can be selected from one or more of the sequences listed in Table 1.

Disclosed herein, are gRNA sequences. Also disclosed herein, are gRNA molecules that can target one or more molecules in a MSUT2 gene. The disclosed gRNA sequences can be specific for one or more desired target sequences. In some aspects, the gRNA sequence can hybridize with a target sequence of a DNA molecule or locus in a cell. In an aspect, the gRNA sequence hybridizes to one or more target or targets sequences corresponding to a MSUT2 gene. In some aspects, the cell can be a eukaryotic cell. In some aspects, the target sequences can be selected from one or more of the sequences listed in Table 1. In some aspects, the cell can be a mammalian or human cell. In some aspects, the cell can be a mesenchymal stem cell. In some aspects, the cell can be a neuron. In some aspects, the cell can be a brain cell. In some aspects, the cell can be any cell that can be delivered therapeutically to the brain, including but not limited to stem cells. For direct gene therapy and delivery to the brain, the cell type can be any cell type in the brain, including but not limited to neurons, oligodendrocytes, microglia, and astrocytes. In an aspect, gRNA sequences target one or more cell type in the brain.

In some aspects, the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA locus. In some aspects, the CRISPR-Cas system and vectors disclosed herein comprise one or more gRNA sequences. In some aspects, the gRNA sequences are listed in Table 2. In some aspects, the target sequences can be selected from one or more of the sequences listed in Table 1. In some aspects, the CRISPR-Cas system and vectors disclosed herein comprise 2, 3, 4 or more gRNA sequences. In some aspects, the CRISPR-Cas system and/or vector described herein comprises 4 gRNA sequences in a single system. In some aspects, the gRNA sequence can comprise 10-30 bp, 15-25 bp, 17-24 bp or any other fragment of the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33. In some aspects, the gRNA sequence comprises a sequence having 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33 or a fragment thereof.

In some aspects, the gRNA molecule disclosed herein can target a nucleic acid sequence that can encode the MSUT2 gene. In some aspects, the nucleic acid sequence that can encode the MSUT2 gene can comprises one or more of: a sequence encoding an amino acid sequence of the MSUT2 gene, a sequence encoding the amino acid sequence of the MSUT2 gene comprising non-translated sequence, or a sequence encoding the amino acid sequence of the MSUT2 gene comprising non-transcribed sequence. In some aspects, the nucleic acid that encodes the MSUT2 gene can correspond to human gene ID: 79882 or mouse gene ID: 75553.

In some aspects, the gRNA molecule can be configured to provide a Cas9 molecule-mediated cleavage event in the nucleic acid that encodes the MSUT2 gene. In some aspects, the gRNA molecule can target the sequence encoding an amino acid sequence of the MSUT2 gene; can be configured to provide a Cas9 molecule-mediated cleavage event in the sequence encoding an amino acid sequence of the MSUT2 gene; or can comprise a targeting domain configured to provide a Cas9 molecule-mediated cleavage event in the sequence encoding an amino acid sequence of the MSUT2 gene.

The compositions described herein can include a nucleic acid encoding a RNA-directed nuclease. The RNA-directed nuclease can be a CRISPR-associated endonuclease. In some aspects, the RNA-directed nuclease can be a Cas9 nuclease or protein. In some aspects, the Cas9 nuclease or protein can have a sequence identical to the wild-type Staphylococcus aureus sequence. In some aspects, the Cas9 nuclease or protein can be a sequence for other species including, for example, Streptococcus pyrogenes or other Streptococcus species, such as thermophilus; Psuedomona aeruginosa, Escherichia coli, or other sequenced bacteria genomes and archaea, or other prokaryotic microorganisms. In some aspects, the wild-type Staphylococcus aureus sequence can be modified. In some aspects, the nucleic acid sequence can be codon optimized for efficient expression in eukaryotic cells.

Disclosed herein, are CRISPR-Cas systems, referred to as CRISPRi (CRISPR interference), that utilizes a nuclease-dead version of Cas9 (dCas9). In some aspects, the dCas9 can be used to repress expression of one or more target sequences (e.g., mammalian suppressor of tauopathy 2 (MSUT2)). In some aspects, the target sequences can be selected from one or more of the sequences listed in Table 1. Instead of inducing cleavage, dCas9 tightly binds to the DNA sequence, and when targeted inside an actively transcribed gene, sterically hinders RNA pol II progression leading to efficient transcriptional repression.

In some aspects, the CRISPR system can be used in which the nuclease has been deactivated. Further, a Krueppel-associated box (KRAB) or p300 core can be attached. In some aspects, the KRAB is attached to downregulate one or more genes in a cell. In some aspects, the p300 core is attached to upregulate one or more genes in a cell.

In some aspects, the CRISPR-Cas system described herein can be used to downregulate a gene in a cell. In an aspect, the expression of one or more genes (or gene products) can be decreased.

In some aspects, the vector can comprise a regulatory element operably linked to an enzyme-coding sequence encoding a CRISPR enzyme (e.g., a Cas protein). In some aspects, the CRISPR enzyme can be Cas9 and can be from Streptococcus pyogenes, Streptococcus thermophiles, Treponema Centicola or Staphylococcus aureus. In some aspects, the Cas9 can be dCas9. In some aspects, the Cas9 protein can be codon optimized for expression in the cell.

In some aspects, dCas9 can be used to silence or inhibit one or more target genes (e.g., MSUT2). For example, dCas9 can be used to silence one or more genes through steric hindrance with or without an attached domain, such as KRAB. dCas9 is the protein that interacts with gRNAs to place the desired editing proteins to specific sites. dCas9 can be used to silence (downregulate or turn off one or more genes). In some aspects, the dCas9 can be attached to KRAB to knockdown, silence or downregulate one or more genes Other proteins can be further attached to dCas9 or included in the CRISPR-Cas system and/or vectors described herein. For example, T2A, a self-cleaving peptide, can be included. T2A allows selection markers (e.g., GFP, fluorescent proteins, antibiotics) to also be attached. The attachment of such markers can be included to permit detection or selection of cells expressing the CRISPR-Cas system and/or vectors described herein.

TABLE 1 Examples of Target Sequences Target Name SEQ Gene Sequence ID NO. MSUT2/ crRNA_human 5′-AATTTATCGA 1 ZC3H14 and mouse CCACCTGCAAG-3′ MSUT2 E6 MSUT2/ crRNA_mouse 5′-TACTGGCCTGC 2 ZC3H14 MSUT2 E13 CTGTAAAAAT-3′ MSUT2/ crRNA_mouse 5′-GGCCTGCCTGT 3 ZC3H14 MSUT2 E13 AAAAATGGGG-3′ MSUT2/ crRNA_mouse 5′-GCCACCAAGAC 4 ZC3H14 MSUT2 E16 ACGCCTTGAA-3′ MSUT2/ MSUT2 sgRNA 5′-ATTAGACACTT 5 ZC3H14 3′UTR#1 CAGATAGAT-3′

TABLE 2 Examples of Guide RNA Sequences (gRNAs) SEQ ID Target Gene Name Sequence NO. MSUT2/ZC3H14 sgRNA_human 5′-GAAUUUAUCGACCACCUGCAAGCAAAG 6 and mouse UUUUAGUACUCUGGAAACAGAAUCUACU MSUT2 E6 AAAACAAGGCAAAAUGCCGUGUUUAUCU CGUCAACUUGUUGGCGAGAUUUUU-3′ MSUT2/ZC3H14 sgRNA_human 5′-GAAUUUAUCGACCACCUGCAAG-3′ 28 and mouse MSUT2 E6 MSUT2/ZC3H14 sgRNA_ mouse 5′-GGCCUGCCUGUAAAAAUGGGGCAAAGU 7 MSUT2E13 UUUAGUACUCUGGAAACAGAAUCUACUA AACAAGGCAAAAUGCCGUGUUUAUCUCG UCAACUUGUUGGCGAGAUUUUU-3′ MSUT2/ZC3H14 sgRNA_ mouse 5′-GGCCUGCCUGUAAAAAUGGGG-3′ 30 MSUT2E13 MSUT2/ZC3H14 sgRNA_ mouse 5′-GCCACCAAGACACGCCUUGAACAAAGU 8 MSUT2E16 UUUAGUACUCUGGAAACAGAAUCUACUA AAACAAGGCAAAAUGCCGUGUUUAUCUC GUCAACUUGUUGGCGAGAUUUUU-3′ MSUT2/ZC3H14 sgRNA_ mouse 5′-GCCACCAAGACACGCCUUGAA-3′ 31 MSUT2E16 MSUT2/ZC3H14 sgRNA 5′-AUUAGACACUUCAGAUAGAUCUGUUU 9 MSUT2 UTR#1 UAGAGCUAGAAAUAGCAAGUUAAAAUAA GGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGCUUUU-3′ MSUT2/ZC3H14 sgRNA 5′-AUUAGACACUUCAGAUAGAU-3′ 32 MSUT2 UTR#1 MSUT2/ZC3H14 sgRNA_mouse 5-GUACUGGCCUGCCUGUAAAAAUCAAAG 33 MSUT2E13 UUUUAGUACUCUGGAAACAGAAUCUACU AAAACAAGGCAAAAUGCCGUGUUUAUCU CGUCAACUUGUUGGCGAGAUUUUU-3′ MSUT2/ZC3H14 sgRNA_mouse 5′-GUACUGGCCUGCCUGUAAAAAU-3′ 29 MSUT2E13

Also, disclosed herein are small molecules. In some aspects, the composition can comprise a small molecule. In an aspect, the small molecule can be

In an aspect, the small molecule (or composition comprising the small molecule) can reduce accumulation of phosphorylated and aggregated human tau protein in a subject. In an aspect, the subject has Alzheimer's disease or dementia. Disclosed herein are compositions comprising a guide RNA sequence selected from the group consisting of SEQ ID NOs: 6, 7, 8, 9, 28, 29, 30, 31, 32 and 33. Also, disclosed herein are compositions comprising an siRNA sequence. Disclosed herein are compositions comprising

(SEQ ID NO: 10) AUGAUGCAAAGUGUACUAAACCAG, (SEQ ID NO: 11) AUGAUGCAAAGUGUACUAAACCAGAUU, (SEQ ID NO: 12) AUGAUGCAAAGUGUACUAAACCAGAU, (SEQ ID NO: 13) AUGAUGCAAAGUGUACUAAACCA, (SEQ ID NO: 14) AUAUGAUGCAAAGUGUACUAAACCAG, or (SEQ ID NO: 15) UAUGAUGCAAAGUGUACUAAACCAG.

Any of the compositions disclosed herein can further comprise a pharmaceutically acceptable carrier. In some aspects, the pharmaceutically acceptable carrier for the siRNA molecule can be buffered saline. In some aspects, the pharmaceutically acceptable carrier for the small molecule can be water or DMSO. In an aspect, the pharmaceutically acceptable carrier can comprise a lipid-based or polymer-based colloid. In some aspects, the colloid can be a liposome, a hydrogel, a microparticle, a nanoparticle, or a block copolymer micelle. In some aspects, the compositions described herein can be formulated for intravenous, subcutaneous, intrathecal, intramuscular, oral or intraperitoneal administration.

Methods

Methods of designing gRNAs. In some aspects, a publically available tool, such as the UCSC genome browser (GRCh37/hg19), can be used to select sequences for the 5′-UTR and the promoter region, 1000 base pairs upstream that can be entered into the CRISPR design tool (crispr.mit.edu). The design tool outputs 20 base pair gRNAs that are followed on their 3′ end by the PAM sequence NNGRRT, which is specific to the CRISPR-Cas9 system derived from Streptococcus aureus. The selected gRNAs can then be entered into the BLAT tool of the UCSC genome browser to inspect for overlap of gRNAs with DNAse hypersensitivity sites to ensure overlap. Any site that has DNAse hypersensitivity value above 0.01 can be targeted with a guide if one is available from the list of guides generated as described above. Additionally, any site that shows greater than 10 transcription factor binding sites within a region, as determined from ChiP-seq, can also be considered. Generally, the DNAse hypersensitivity data is consistent with these regions. Using the criteria described above, gRNAs (e.g., 4-7 gRNAs) that are spaced at least 100 base pairs apart can be selected for performing targeted gene repression and screening. In an aspect, MSUT2 gRNAs guides can be screened using the method disclosed herein. In an aspect, gRNA sequences from the promoter region and 5′-UTR (crispr.mit.edu) can be selected. In an aspect, gRNA sequences are 20 bp in length followed by a PAM sequence (e.g., NNGRRTNGG). In an aspect, gRNA sequences with the least off-target sequences and those that overlap with DNase sensitivity peaks can be selected.

In some aspects, the design tool outputs 20 base pair gRNAs that are followed on their 3′ end by the PAM sequence NGG, which is specific to the CRISPR-Cas9 system derived from Streptococcus pyogenes. The selected gRNAs can then be entered into the BLAT tool of the UCSC genome browser to inspect for overlap of gRNAs with DNAse hypersensitivity sites to ensure overlap. Any site that has DNAse hypersensitivity value above 0.01 can be targeted with a guide if one is available from the list of guides generated as described above. Additionally, any site that shows greater than 10 transcription factor binding sites within a region, as determined from ChiP-seq, can also be considered. Generally, the DNAse hypersensitivity data is consistent with these regions. Using the criteria described above, gRNAs (e.g., 4-7 gRNAs) that are spaced at least 100 base pairs apart can be selected for performing targeted gene repression and screening. In an aspect, MSUT2 gRNAs guides can be screened using the method disclosed herein. In an aspect, gRNA sequences from the promoter region and 5′-UTR (crispr.mit.edu) can be selected. In an aspect, gRNA sequences are 20 bp in length followed by a PAM sequence (e.g., NGG). In an aspect, gRNA sequences with the least off-target sequences and those that overlap with DNase sensitivity peaks can be selected.

Disclosed herein are methods of modulating expression of a gene in a cell. The method can include one or more of the following steps. First, introducing into a cell, a first nucleic acid. The first nucleic acid can encode a guide RNA comprising a DNA-binding domain. The nucleic acid can be operably linked to a regulatory element. The guide RNA described herein can be complementary to a target nucleic acid sequence disclosed herein comprising the gene. Next, a second nucleic acid encoding a transcriptional regulator protein or domain that modulates the target nucleic acid expression can be introduced into the cell. The second nucleic acid can further include a gRNA-binding domain. The second nucleic acid can be operably linked to a regulatory element. A third nucleic acid encoding a Cas9 (e.g., a deactivated nuclease (dCas9)) protein can be introduced. In an aspect, nuclease function can be removed. The third nucleic acid can be operably linked to a regulatory element. The Cas9 protein (e.g., dCas9) can interact with the guide RNA, and can be fused to the transcriptional regulator protein. The cell can then produce the guide RNA. The guide RNA can bind to the dCas9 protein and the transcriptional regulator protein or domain fused to the DNA-binding domain, and direct the complex (e.g., gRNA/dCas9 complex; the combined product of the gRNA and dCas9 interacting) to the DNA regulatory element encoded in the DNA-binding domain. The guide RNA and the dCas9 protein, for example, can co-localize to the target nucleic acid sequence. The transcriptional regulator protein or domain can modulate (increase or decrease) expression of the gene. The gRNA sequence can selected from the group listed in Table 2.

Disclosed herein, are methods for introducing into a cell a CRISPR-Cas system. In some aspects, the CRISPR-Cas system can include one or more vectors described herein. In some aspects, the method can include one or more vectors. For example, the vector can comprise a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA. In some aspects, the gRNA can hybridize with a target sequence of a DNA molecule in a cell. In some aspects, the vector can also include a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease. In some aspects, the promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA and the regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease can be located on the same or different vectors of the same system. In some aspects, the method also includes a step wherein the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA molecule. In some aspects, the gRNA sequence can be selected from the group listed in Table 2. In some aspects, the target sequence can be selected from one or more of the sequences listed in Table 1.

Disclosed herein, are methods for introducing into a cell a vector. In some aspects, the vector can include a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system gRNA. In some aspects, the vector can also include a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease. In some aspects, the gRNA sequence can be selected from the group listed in Table 2.

Disclosed herein, are methods for inducing site-specific DNA cleavage in a cell. The method can comprise contacting a cell with a guide RNA. The guide RNA can be selected from the group listed in Table 2. The guide RNA can include a sequence capable of binding to a target DNA. The method can further comprise the following step: contacting the cell with a Cas9 protein. In an aspect, the DNA can be in a cell. In an aspect, the cell can be a eukaryotic cell. In an aspect, the cell can be in an individual. In an aspect, the individual can be a human.

The method steps described herein can be carried out simultaneously or sequentially in any order. In some aspects, the DNA can be in a cell. In some aspects, the cell can be a eukaryotic cell. In some aspects, the cell can be in an individual. In some aspects, the individual can be a human.

Method of Treatment

The methods disclosed herein can be useful for the treatment of a subject with Alzheimer's disease or dementia. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In an aspect, the therapeutically effective amount can reduce accumulation of phosphorylated and aggregated human tau

The methods disclosed herein can be useful for inhibiting expression of a MSUT2 polynucleotide. In some aspects, the method can inhibit expression of a MSUT2 polynucleotide in a subject. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the method can comprise contacting a cell with a MSUT2 inhibitor. In some aspects, the suppressor of MSUT2 can reduce accumulation of phosphorylated and aggregated tau. In some aspects, the expression of the MSUT2 polynucleotide can be inhibited or suppressed by a small molecule. In some aspects, the small molecule can inhibit the binding of poly(A) RNA to the MSUT2 polynucleotide. In some aspects, the cell can be a mammalian cell. In some aspects, the mammalian cell can be a brain cell.

The methods disclosed herein can be useful for reducing phosphorylated and aggregated human tau protein in a subject. The methods can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor.

The methods disclosed herein can be useful for suppressing expression of a MSUT2 polynucleotide. In some aspects, the method can suppress expression of a MSUT2 polynucleotide in a subject. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the method can comprise contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the suppressor of tauopathy 2 (MSUT2) can reduce accumulation of phosphorylated and aggregated tau. In some aspects, the expression of the MSUT2 polynucleotide can be inhibited or suppressed by a small molecule. In some aspects, the small molecule can inhibit the binding of poly(A) RNA to the MSUT2 polynucleotide. In some aspects, the cell can be a mammalian cell. In some aspects, the mammalian cell can be a brain cell.

The methods disclosed herein can be useful for potentiating a neuroinflammatory response to a pathological tau protein. In some aspects, the method can potentiate a neuroinflammatory response to a pathological tau protein in a subject. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the method can comprise contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the suppressor of tauopathy 2 (MSUT2) can reduce accumulation of phosphorylated and aggregated tau. In some aspects, the cell can be a mammalian cell. In some aspects, the mammalian cell can be a brain cell.

The methods disclosed herein can be useful for decreasing astrocytosis or microgliosis. In some aspects, the method can decrease astrocytosis or microgliosis in a subject. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the method can comprise contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the suppressor of tauopathy 2 (MSUT2) can reduce accumulation of phosphorylated and aggregated tau. In some aspects, the cell can be a mammalian cell. In some aspects, the mammalian cell can be a brain cell.

The methods disclosed herein can be useful for reducing neuroinflammation. In some aspects, the method can reduce neuroinflammation in a subject. The method can comprise administering to a subject with Alzheimer's disease or dementia a therapeutically effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the method can comprise contacting a cell with a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the suppressor of tauopathy 2 (MSUT2) can reduce accumulation of phosphorylated and aggregated tau. In some aspects, the expression of the MSUT2 polynucleotide can be inhibited or suppressed by a small molecule. In some aspects, the small molecule can inhibit the binding of poly(A) RNA to the MSUT2 polynucleotide. In some aspects, the cell can be a mammalian cell. In some aspects, the mammalian cell can be a brain cell.

In some aspects, the subject has Alzheimer's disease. In some aspects, the subject has dementia. In some aspects, the subject has mild-moderate Alzheimer's disease. In some aspects, the subject has moderate-severe Alzheimer's disease. Alzheimer's disease typically progresses slowly in three general stages, mild (early stage), moderate (middle stage) and severe (late stage). In mild Alzheimer's disease (early stage), subjects can still function independently but may notice that they are having memory lapses such as forgetting familiar words or the location of everyday objects. During moderate Alzheimer's disease (middle stage), subjects may have greater difficulty performing tasks (e.g., paying bills) and confusing words, but may still remember significant details about their life. In addition, subjects in this stage may feel moody or withdrawn, are at an increased risk of wandering and becoming lost, and can exhibit personality and behavioral changes including suspiciousness and delusions or compulsive, repetitive behavior. In severe Alzheimer's disease (late stage), subjects lose the ability to respond to their environment, to carry on a conversation and eventually, to control movement. Also, during this severe stage, subjects need extensive help with daily activities and have increasing difficulty communicating. In some aspects, the subject has an Alzheimer's-related dementia. In an aspect, the Alzheimer's-related dementia can be progressive supranuclear palsy, chronic traumatic encephalopathy, frontotemporal lobar degeneration, or other tauopathy disorders. The methods disclosed herein can be effective for targeting one or more genes, including mammalian suppressor of tauopathy 2 (MSUT2). In some aspects, the methods also include the step of administering a therapeutic effective amount of a mammalian suppressor of tauopathy 2 (MSUT2) inhibitor. In some aspects, the MSUT2 inhibitor can be a small interfering RNA (siRNA), a guide RNA, a small molecule, an antisense oligonucleotide or an aptamer. In some aspects, the antisense oligonucleotide can be

(SEQ ID NO: 16) ATGATGCAAAGTGTACTAAACCAG, (SEQ ID NO: 17) ATGATGCAAAGTGTACTAAACCAGA, (SEQ ID NO: 18) ATGATGCAAAGTGTACTAAACCAGATT, (SEQ ID NO: 19) ATGATGCAAAGTGTACTAAACCAG, (SEQ ID NO: 20) AATATGATGCAAAGTGTACTAAAC, or (SEQ ID NO: 21) ATATGATGCAAAGTGTACTAAACCAG.

In some aspects, the methods of treating a subject can comprise contacting a cell or a subject with an effective amount of a gRNA molecule. In some aspects, the methods can further comprise altering the sequence of the target nucleic acid. In some aspects, the cell can be a vertebrate, a mammalian or a human cell. In some aspects, the cell can be a brain cell.

In some aspects, the methods also include the step of administering a therapeutic effective amount of one or more of the compositions disclosed herein (e.g., a CRISPR-Cas system comprising one or more vectors comprising: a) a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA), wherein the gRNA hybridizes with a target sequence of a DNA locus in a cell; and b) a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease, wherein components a) and b) are located on the same or different vectors of the same system, wherein the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA locus; wherein the gRNA sequence is selected from the group listed in Table 2. In some aspects, the gRNA sequence can comprise 10-30 bp, 15-25 bp, 17-24 bp or any other fragment of the sequences set forth in SEQ ID NOs: 6, 7, 8, 9 and 33. In some aspects, the gRNA sequence comprises a sequence having 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33 or a fragment thereof. In some aspects, the therapeutically effective amount can reduce accumulation of phosphorylated and aggregated human tau. In some aspects, the subject can be identified as being in need of treatment before the administering step. In some aspects, the subject can be a human.

In some aspects, the MSUT2 inhibitor can potentiate the neuroinflammatory response to pathological tau. In some aspects, the MSUT2 inhibitor can decrease astrocytosis and microgliosis.

In some aspects, the gRNA can target and hybridize to a MSUT2 target sequence. In some aspects, the target sequences can be selected from one or more of the sequences found with the following identifier: mouse gene ID: 75553; Human gene ID is: 79882. In some aspects, the MSUT2 target sequence can be

(SEQ ID NO: 1) AATTTATCGACCACCTGCAAG, (SEQ ID NO: 2) TACTGGCCTGCCTGTAAAAAT, (SEQ ID NO: 3) GGCCTGCCTGTAAAAATGGGG, (SEQ ID NO: 4) GCCACCAAGACACGCCTTGAA, or (SEQ ID NO: 5) ATTAGACACTTCAGATAGAT.

In some aspects, the gRNA sequence can be selected from the group consisting of

(SEQ ID NO: 6) GAAUUUAUCGACCACCUGCAAGCAAAGUUUUAGUA CUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAU GCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUU UU, (SEQ ID NO: 7) GGCCUGCCUGUAAAAAUGGGGCAAAGUUUUAGUAC UCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUG CCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUU U, (SEQ ID NO: 8) GCCACCAAGACACGCCUUGAACAAAGUUUUAGUAC UCUGGAAACAGAAUCUACUAAAACAAGGCAAAAUG CCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUUU U, (SEQ ID NO: 9) AUUAGACACUUCAGAUAGAUCUGUUUUAGAGCUAG AAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCA ACUUGAAAAAGUGGCACCGAGUCGGUGCUUUU, (SEQ ID NO: 33) GUACUGGCCUGCCUGUAAAAAUCAAAGUUUUAGUA CUCUGGAAACAGAAUCUACUAAAACAAGGCAAAAU GCCGUGUUUAUCUCGUCAACUUGUUGGCGAGAUUU UU, (SEQ ID NO: 28) GAAUUUAUCGACCACCUGCAAG (SEQ ID NO: 29) GUACUGGCCUGCCUGUAAAAAU (SEQ ID NO: 30) GGCCUGCCUGUAAAAAUGGGG (SEQ ID NO: 31) GCCACCAAGACACGCCUUGAA, and (SEQ ID NO: 32) AUUAGACACUUCAGAUAGAU.

In some aspects, the siRNA can consist of

(SEQ ID NO: 10) AUGAUGCAAAGUGUACUAAACCAG, (SEQ ID NO: 11) AUGAUGCAAAGUGUACUAAACCAGAUU, (SEQ ID NO: 12) AUGAUGCAAAGUGUACUAAACCAGAU, (SEQ ID NO: 13) AUGAUGCAAAGUGUACUAAACCA, (SEQ ID NO: 14) AUAUGAUGCAAAGUGUACUAAACCAG, or (SEQ ID NO: 15) UAUGAUGCAAAGUGUACUAAACCAG.

In some aspects, the small molecule can be

In some aspects, the methods can further include the step of identifying a subject (e.g., a human patient) who has Alzheimer's disease or dementia and then providing to the subject a composition comprising the CRISPR-Cas system or vector, or a MSUT2 inhibitor as disclosed herein. In some aspects, the subject has an Alzheimer's-related dementia. In an aspect, the Alzheimer's-related dementia can be progressive supranuclear palsy, chronic traumatic encephalopathy, frontotemporal lobar degeneration, or other tauopathy disorders. In some aspects, the subject can be identified using standard clinical tests known to those skilled in the art. While a definite AD diagnosis requires post-mortem examination, skilled clinicians can conduct an evaluation of cognitive function with over 95% accuracy. Examples of tests for diagnosing Alzheimer's disease or dementia include Mini-Mental State Examination (MMSE), Mini-Cog© Score, Alzheimer's Disease Composite Score (ADCOMS), Alzheimer's Disease Assessment Scale-cognitive subscale (ADAS-Cog) and Clinicial Dementia Rating Sum of Boxes (CDR-SB).

The therapeutically effective amount can be the amount of the composition administered to a subject that leads to a full resolution of the symptoms of the condition or disease, a reduction in the severity of the symptoms of the condition or disease, or a slowing of the progression of symptoms of the condition or disease. The methods described herein can also include a monitoring step to optimize dosing. The compositions described herein can be administered as a preventive treatment or to delay or slow the progression of degenerative changes.

The compositions disclosed herein can be used in a variety of ways. For instance, the compositions disclosed herein can be used for direct delivery of modified therapeutic cells, or adeno-associated virus. The compositions disclosed herein can be used or delivered or administered at any time during the treatment process. The compositions described herein including cells or a virus can be delivered to the one or more brain regions, one or more brain cells, or to brain regions or brain cells to stop or prevent one or more signs of symptoms of the disease or condition in an adjacent brain region or brain cell.

The dosage to be administered depends on many factors including, for example, the route of administration, the formulation, the severity of the patient's condition/disease, previous treatments, the patient's size, weight, surface area, age, and gender, other drugs being administered, and the overall general health of the patient including the presence or absence of other diseases, disorders or illnesses. Dosage levels can be adjusted using standard empirical methods for optimization known by one skilled in the art. Administrations of the compositions described herein can be single or multiple (e.g., 2- or 3-, 4-, 6-, 8-, 10-, 20-, 50-, 100-, 150-, or more fold). Further, encapsulation of the compositions in a suitable delivery vehicle (e.g., polymeric microparticles or implantable devices) can improve the efficiency of delivery.

The therapeutically effective amount of the compositions described herein can include a single treatment or a series of treatments (i.e., multiple treatments or administered multiple times). Treatment duration using any of compositions disclosed herein can be any length of time, such as, for example, one day to as long as the life span of the subject (e.g., many years). For instance, the composition can be administered daily, weekly, monthly, yearly for a period of 5 years, ten years, or longer. The frequency of treatment can vary. For example, the compositions described herein can be administered once (or twice, three times, etc.) daily, weekly, monthly, or yearly for a period of 5 years, ten years, or longer.

In some aspects, the compositions disclosed herein can also be co-administered with another therapeutic agent. In some aspects, the methods disclosed herein can further comprise administering a cholinesterase inhibitor to the subject. In some aspects, the cholinesterase inhibitor can be galantamine, rivastigmine or donepezil. In some aspects, the methods disclosed herein can further comprise administering an anti-inflammatory therapy to the subject.

In some aspects, the methods disclosed herein also include treating a subject having Alzheimer's disease or dementia. In some aspects, the methods disclosed herein can include the step of determining MSUT2 levels in a subject. In some aspects, the disclosed methods can further include the step of administering to the subject a pharmaceutical composition comprising a nucleic acid sequence encoding a CRISPR-associated endonuclease (e.g., deactivated endonuclease) and one or more guide RNAs, wherein the guide RNA is selected from the group listed in Table 2. In some aspects, the CRISPR-associated endonuclease is optimized for expression in a human cell.

Pharmaceutical Compositions

As disclosed herein, are pharmaceutical compositions, comprising the compositions disclosed herein. In an aspect, the pharmaceutical composition can comprise any of gRNA molecules disclosed herein. In an aspect, the pharmaceutical composition can comprise any of the small molecules, aptamers (e.g., DNA and RNA), antisense oligonucleotides or siRNAs disclosed herein. For example, disclosed are pharmaceutical compositions, comprising a vector or CRISPR-Cas system comprising one or more vectors comprising: a) a promoter operably linked to one or more nucleotide sequences encoding a CRISPR-Cas system guide RNA (gRNA), wherein the gRNA hybridizes with a target sequence of a DNA locus in a cell; and b) a regulatory element operably linked to a nucleotide sequence encoding a RNA-directed nuclease, wherein components a) and b) are located on the same or different vectors of the same system, wherein the gRNA targets and hybridizes with the target sequence and directs the RNA-directed nuclease to the DNA locus; wherein the gRNA sequence is selected from the group listed in Table 2. In some aspects, the gRNA sequence can comprise 10-30 bp, 15-25 bp, 17-24 bp or any other fragment of the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33. In some aspects, the gRNA sequence comprises a sequence having 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% identity to the sequences set forth in SEQ ID NOs: 6, 7, 8, 9, and 33 or a fragment thereof. In some aspects, the target sequence can be selected from one or more of the sequences listed in Table 1. In some aspects, the pharmaceutical compositions comprise the any one of the CRISPR-Cas systems disclosed herein. In some aspects, the pharmaceutical composition comprises the nucleic acid sequence of any of the vectors or CRISPR-Cas systems disclosed herein. In some aspects, the pharmaceutical compositions further comprise a pharmaceutically acceptable carrier.

As used herein, the term “pharmaceutically acceptable carrier” refers to solvents, dispersion media, coatings, antibacterial, isotonic and absorption delaying agents, buffers, excipients, binders, lubricants, gels, surfactants that can be used as media for a pharmaceutically acceptable substance. The pharmaceutically acceptable carriers can be lipid-based or a polymer-based colloid. Examples of colloids include liposomes, hydrogels, microparticles, nanoparticles and micelles. The compositions can be formulated for administration by any of a variety of routes of administration, and can include one or more physiologically acceptable excipients, which can vary depending on the route of administration. Any of the nucleic acids, vectors, gRNAs, siRNAs, aptamers, antisense oligonucleotides and small molecules described herein can be administered in the form of a pharmaceutical composition.

As used herein, the term “excipient” means any compound or substance, including those that can also be referred to as “carriers” or “diluents.” Preparing pharmaceutical and physiologically acceptable compositions is considered routine in the art, and thus, one of ordinary skill in the art can consult numerous authorities for guidance if needed. The compositions can also include additional agents (e.g., preservatives).

The pharmaceutical compositions as disclosed herein can be prepared for oral or parenteral administration. Pharmaceutical compositions prepared for parenteral administration include those prepared for intravenous (or intra-arterial), intramuscular, subcutaneous, intrathecal or intraperitoneal administration. Paternal administration can be in the form of a single bolus dose, or may be, for example, by a continuous pump. In some aspects, the compositions can be prepared for parenteral administration that includes dissolving or suspending the CRISPR-Cas systems, nucleic acids, polynucleic sequences, vectors or small molecules in an acceptable carrier, including but not limited to an aqueous carrier, such as water, buffered water, saline, buffered saline (e.g., PBS), and the like. One or more of the excipients included can help approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents, detergents, and the like. Where the compositions include a solid component (as they may for oral administration), one or more of the excipients can act as a binder or filler (e.g., for the formulation of a tablet, a capsule, and the like). Where the compositions are formulated for application to the skin or to a mucosal surface, one or more of the excipients can be a solvent or emulsifier for the formulation of a cream, an ointment, and the like.

In some aspects, the compositions disclosed herein are formulated for oral, intramuscular, intravenous, subcutaneous or intraperitoneal administration.

The pharmaceutical compositions can be sterile and sterilized by conventional sterilization techniques or sterile filtered. Aqueous solutions can be packaged for use as is, or lyophilized, the lyophilized preparation, which is encompassed by the present disclosure, can be combined with a sterile aqueous carrier prior to administration. The pH of the pharmaceutical compositions typically will be between 3 and 11 (e.g., between about 5 and 9) or between 6 and 8 (e.g., between about 7 and 8). The resulting compositions in solid form can be packaged in multiple single dose units, each containing a fixed amount of the above-mentioned agent or agents, such as in a sealed package of tablets or capsules. The composition in solid form can also be packaged in a container for a flexible quantity, such as in a squeezable tube designed for a topically applicable cream or ointment. The compositions can also be formulated as powders, elixirs, suspensions, emulsions, solutions, syrups, aerosols, lotions, creams, ointments, gels, suppositories, sterile injectable solutions and sterile packaged powders. The active ingredient can be nucleic acids or vectors described herein in combination with one or more pharmaceutically acceptable carriers. As used herein “pharmaceutically acceptable” means molecules and compositions that do not produce or lead to an untoward reaction (i.e., adverse, negative or allergic reaction) when administered to a subject as intended (i.e., as appropriate).

In some aspects, the CRISPR-Cas system, vectors, gRNAs and nucleic acid sequences as disclosed herein can be delivered to a cell of the subject. In some aspects, such action can be achieved, for example, by using polymeric, biodegradable microparticle or microcapsule delivery vehicle, sized to optimize phagocytosis by phagocytic cells (e.g., macrophages).

In some aspects, the formulations include any that are suitable for the delivery of a virus (e.g., adeno-associated virus) and cells. In an aspect, the route of administration includes but is not limited to direct injection into the brain. Such administration can be done without surgery, or with surgery.

Method of Screening

Disclosed herein are methods of screening compounds capable of inhibiting MSUT2 binding to poly(A) RNA. In some aspects, the method can comprise contacting at least one candidate compound, poly(A) RNA and polyadenylate-binding nuclear protein 1 (PABPN1) under conditions in which PABPN1 is capable of stimulating RNA polyadenylation in the absence of the candidate compound. In some aspects, the method can comprise determining whether the candidate compound inhibits MSUT2 binding to poly(A) RNA. In some aspects, the method can comprise selecting the candidate compound which inhibits MSUT2 binding to poly(A) RNA. In some aspects, the inhibition of MSUT2 binding to poly(A) RNA can be measured by RNA polyadenylation. In some aspects, the candidate compound selected can inhibit formation of a macromolecular complex, wherein the macromolecular complex can comprise MSUT2, PABPN1 and poly(A) RNA. In some aspects, the candidate compound can be purified. In some aspects, the candidate compound can be isolated.

Disclosed herein are methods for screening compounds for pharmacological intervention in tauopathy disorders. In some aspects, the method can comprise providing an assay for MSUT2 to bind to poly(A) RNA and its modulation of RNA polyadenylation. In some aspects, the method can comprise providing a purified or non-purified compound or purified or non purified mixture of compounds. In some aspects, the method can comprise screening the purified or non-purified compound or purified or non-purified mixture of compounds in an environment that can allow for inhibition of MSUT2 binding to poly(A) RNA by the purified or non-purified compound or purified or non-purified mixture of compounds in the assay. In some aspects, the method can comprise isolating the one or more compounds that inhibit MSUT2 binding to poly(A) RNA. In some aspects, the method can comprise the inhibition of MSUT2 binding to poly(A) RNA is measured by RNA polyadenylation. In some aspects, the assay can comprise forming a macromolecular complex that can comprise MSUT2, PABPN1, and poly(A) RNA.

In an aspect, the tauopathy disorder can be a degenerative disorder. Example of tauopathy disorders include but are not limited to primary tauopathies (e.g., Frontotemporal Lobar Degeneration Frontotemporal Dementia (FTLD), primary progressive aphasia, including atypical dopaminergic-resistant Parkinsonian syndromes with prominent extra-pyramidal symptoms and corticobasal syndrome; and secondary tauopathies.

Kits

The kits described herein can include any combination of the compositions (e.g., CRISPR-Cas system or vectors or siRNAs, gRNAs, aptamers, antisense oligonucleotides or small molecules) described above and suitable instructions (e.g., written and/or provided as audio-, visual-, or audiovisual material). In an aspect, the kit comprises a predetermined amount of a composition comprising any one compositions disclosed herein. The kit can further comprise one or more of the following: instructions, sterile fluid, syringes, a sterile container, delivery devices, and buffers or other control reagents.

EXAMPLES Example 1: The Poly(A) Binding Protein MSUT2 Controls Resistance to Both Pathological Tau and Gliosis

Abstract. Lesions composed of pathological tau drive neurodegeneration in Alzheimer's disease and related tauopathies. The mammalian suppressor of tauopathy 2 (MSUT2) gene was identified as a modifier of susceptibility to tau toxicity in multiple model systems. Tau transgenic MSUT2 knockout mice exhibit decreased learning and memory deficits, ameliorated neurodegeneration, and reduced accumulation of pathological tau. Conversely, MSUT2 overexpression in tau transgenic mice drives pathological tau deposition and promotes the neuroinflammatory response to pathological tau. MSUT2 functions as a poly(A) RNA binding protein that antagonizes the canonical nuclear poly(A) binding protein PABPN1. In Alzheimer's disease, MSUT2 abundance predicts age at disease onset and cases with normal levels of MSUT2 exhibit elevated neuroinflammation associated with tau pathology. Also, a similar co-depletion of PABPN1 was observed in the same subset of AD cases suggesting MSUT2 and PABPN1 act together in a macromolecular complex bound to poly(A) RNA. Although MSUT2 and PABPN1 have opposing effects on both tau aggregation and poly(A) tail length, it was found that increased poly(A) tail length does not ameliorate tauopathy, implicating other functions of MSUT2/PABPN1 in their role in tau proteostasis. These findings implicate poly(A) RNA binding proteins as both modulators of pathological tau toxicity in AD and as potential molecular targets for intervention in neurodegeneration in tauopathies.

Results.

Removal of MSUT2 drives neuronal resistance to pathological tau. To test whether MSUT2 function impacts tauopathy in the intact mammalian brain, mice lacking the MSUT2 CCCH finger domains important for SUT-2 function in C. elegans was generated (FIGS. 1A-E). Mice homozygous for this disruption (henceforth, MSUT2 KO mice) are fully viable, grossly normal, exhibit no visible phenotypes, and appear neurologically intact. These mice were crossed with PS19, a well-characterized mouse tauopathy model transgenic for human tau carrying the P301S FTLD mutation (Y. Yoshiyama, et al., Neuron 53, 337-351 (2007)). PS19 mice homozygous for the MSUT2 KO allele were generated and the abundance of tau positive pathological lesions in PS19 mice with or without functional MSUT2 were compared. Since PS19 mice exhibit significant deficits in hippocampal dependent memory tasks (H. Takeuchi, et al., PLoS ONE 6, e21050 (2011)), the neuropathological analysis focused on the hippocampal formation and projecting regions. PS19 mice develop age-dependent neurofibrillary degeneration with a progression of pathological tau deposition similar to that seen in human patients with AD or other tauopathy disorders (Y. Yoshiyama, et al., Neuron 53, 337-351 (2007)). PS19 mice have an abundance of NFT-like inclusions in hippocampal CA1 pyramidal neurons and the entorhinal cortex. In contrast, PS19 mice that are homozygous null for MSUT2 have dramatically reduced numbers of hippocampal NFTs (FIG. 2A and FIG. 1F). Formation of pathological tau progresses from monomeric normal tau, to phosphorylated tau (pTau), to oligomeric and pre-tangle conformations of tau, to fibrillary tau culminating in deposition of mature NFTs. Both pTau and mis-folded tau (MC1 positive) are dramatically reduced in MSUT2 KO/PS19 relative to PS19 animals, especially in neuronal processes of hippocampal subfields stratum lacunosum molecular (SLM) and stratum oriens (SO), as well as in the entorhinal cortex (FIGS. 2B-C, and Fig S2A-B). When MSUT2 is absent, the overall decrease in pTau and MC1+ tau parallels the decrease of NFTs in the hippocampus and entorhinal cortex. Likewise, the MSUT2 KO/PS19 mice do not show the neuronal loss in the CA1 region of the hippocampus that is observed in PS19 mice with intact MSUT2 (FIG. 2D) while loss of MSUT2 alone does not obviously change neuronal abundance in the hippocampus (FIG. 3C). These findings demonstrate that loss of MSUT2 reduces accumulation of pathologic tau and protects against neuronal loss.

Knockout of MSUT2 improves cognitive function in tauopathy mice. MSUT2 KO mice exhibit typical motor function, and appear cognitively similar to wild type mice (FIG. 4 and FIG. 2E). To assess the effect of MSUT2 on PS19 motor activity and behavior, PS19 mice with or without a functional MSUT2 gene (PS19 vs MSUT2 KO/PS19) at 8 months of age (N=32-33 per genotype) were characterized. As in a wild type background, loss of MSUT2 does not alter gross physical parameters, motor function, or spontaneous activity levels of PS19 mice (FIGS. 4B-G), although MSUT2 KO does protect against age related weight loss in PS19 males (FIG. 4D). The cognitive performance of these mice was examined using the Barnes maze assay of hippocampal dependent learning and memory (C. A. Barnes, Journal of comparative and physiological psychology 93, 74-104 (1979), a task at which PS19 animals have a significant and reproducible impairment (FIG. 2E and K. R. Brunden, et al., J Neurosci 30, 13861-13866 (2010); and B. Zhang, et al., J Neurosci 32, 3601-3611 (2012)). MSUT2 KO/PS19 exhibit better performance during the training trials (as measured by time to locate the escape hole), and learn the Barnes maze task faster than their PS19 siblings (FIG. 2E). These data show that loss of MSUT2 function improves cognitive function caused by the mutant tau transgene in PS19 mice.

MSUT2 binds the poly(A) binding protein PABPN1 through multifunctional CCCH domains. To explore the mechanism of MSUT2 function, the C-terminus of MSUT2 and SUT-2 was the focus as this region appears to be an important functional domain for suppressing tauopathy phenotypes (C. R. Guthrie, et al., Hum Mol Genet 18, 1825-1838 (2009); and C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011)). To explore the functional partners of SUT-2 protein, a yeast two-hybrid screen was conducted using the sut-2 CCCH domains as bait. The major SUT-2 binding protein identified representing over 90% of the cDNAs recovered was the homolog of nuclear polyadenylate binding protein PABPN1. PABPN1 binds to the poly(A) tail on mRNAs through its RNA recognition motif (RRM) domain and regulates poly(A) tail length in both yeasts and mammals (U. Kuhn, et al., J Biol Chem 278, 16916-16925 (2003); and A. Banerjee, et al., FEBS J 280, 4230-4250 (2013)). It was demonstrated that a conserved protein-protein interaction between human PABPN1 and MSUT2 proteins using purified recombinant human proteins in an in vitro GST-pulldown assay and showed that the interaction can occur in the absence of detectable RNA (FIG. 5A). The binding of MSUT2 to PABPN1 was validated in a cellular context in situ using a proximity ligation assay on human HEK293 cells (O. Soderberg, et al., Methods 45, 227-232 (2008)) and found MSUT2 binds to PABPN1 predominantly in the nuclear compartment and to a lesser extent the cytoplasm (FIG. 5B). Since CCCH domains can bind both RNA and protein, MSUT2 association with poly(A) RNA was measured using a Surface Plasmon Resonance assay. MSUT2 affinity for poly(A) is approximately 4-fold greater than PABPN1 for a single poly(A) binding site (MSUT2 K_(D)=60±15 nM vs PABPN1 K_(D)=237±21 nM for poly(A)₁₅) (FIG. 5C).

MSUT2 co-localizes with PABPN1 and poly(A) RNA within nuclear speckles. Since MSUT2 binds PABPN1 and poly(A) independently in vitro, the relationship between MSUT2, PABPN1, and poly(A) RNA was examined in cultured human cells. HEK293 cells were immunostained for MSUT2 and PABPN1 and hybridized with poly(A)-specific fluorescent probes. Analysis showed that MSUT2 protein significantly co-localizes with PABPN1 and poly(A) RNA in the nucleus (FIG. 5D, FIGS. 6A-B). To explore whether the speckle-like appearance of MSUT2 and PABPN1 immunostaining represents authentic nuclear speckle localization, MSUT2 and PABPN1 were co-stained with antibodies against SC35, a nuclear splicing factor labeling nuclear speckles and significant co-localization of both MSUT2 and PABPN1 with SC35 within nuclear speckles were observed (FIGS. 6C, D). Also, the localization of MSUT2 and PABPN1 was investigated in normal human brain. Co-immunostaining for MSUT2 and PABPN1 revealed clear nuclear co-localization of PABPN1 and MSUT2 in frontal cortex neurons (FIG. 5E). Taken together, these data support the cellular co-localization of MSUT2 and PABPN1 to poly(A)+ RNA in nuclear speckles consistent with their demonstrated physical interaction with each other and RNA.

MSUT2 and PABPN1 reciprocally regulate tau aggregation. Recent work demonstrated that siRNA knockdown of PABPN1 decreases the poly(A) tail length on bulk mRNAs while knockdown of MSUT2 increases poly(A) tail length, indicating opposing functions of PABPN1 and MSUT2 in polyadenylation (S. M. Kelly, et al., RNA 20, 681-688 (2014); and S. Soucek, et al., Biochim Biophys Acta 1819, 546-554 (2012)). To explore whether the PABPN1/MSUT2 interaction mediates changes in accumulation of pathological tau, tau aggregation was analyzed in cultured human cells (HEK293/tau) constitutively overexpressing human tau in which MSUT2 or PABPN1 were knocked down by gene specific siRNA treatment (FIG. 7A). pTau species in MSUT2 knockdown was decreased as assessed by immunostaining with AT180 monoclonal antibody (Thr231, FIG. 7B vs 7C). Similar quantitative measures show MSUT2 siRNA-mediated knockdown decreases both pTau and tau oligomeric species accumulation as detected by quantitative immunofluorescence with TOC1 (S. M. Ward, et al., J Alzheimers Dis 37, 593-602 (2013)) and MC1 (G. A. Jicha, et al., J Neurosci Res 48, 128-132 (1997) conformation specific monoclonal antibodies (FIG. 7E). In contrast, PABPN1 knockdown exacerbates accumulation of aggregated tau in both assays (FIG. 7B vs 7D, and 7E). Thus, MSUT2 and PABPN1 have reciprocal effects on tau aggregation with MSUT2 promoting tau aggregation while PABPN1 inhibits tau aggregation. Likewise, knockdown of MSUT2 and PABPN1 together has an intermediate tau aggregation phenotype (FIG. 8A). However, knockout of MSUT2 does not alter PABPN1 protein expression level (FIG. 8B) or expression pattern (FIG. 8C). To investigate whether PABPN1 and MSUT2 effects on tau related phenotypes can be attributed to effects on mRNA poly(A) tail length, mRNA poly(A) tail lengths were directly manipulated using mutations in the gene encoding CCR-4, the major mRNA poly(A) deadenylase in C. elegans. Mutations in ccr-4 cause dramatic lengthening of bulk mRNA poly(A) tails in C. elegans (M. Nousch, et al., J Cell Sci 126, 4274-4285 (2013)), similar to what is seen for human MSUT2 knockdown in human cells (S. M. Kelly, et al., RNA 20, 681-688 (2014)). Analysis of tau Tg C. elegans carrying a strong loss of function mutation in ccr-4 demonstrate an enhancement of tauopathy related behavioral deficits (FIG. 7F). In contrast, loss of function mutations in sut-2 strongly suppress accumulation of pathological tau and tau mediated neurodegeneration (C. R. Guthrie, et al., SUT-2 potentiates tau-induced neurotoxicity in Caenorhabditis elegans. Hum Mol Genet 18, 1825-1838 (2009); and C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011)). These data suggest changes in bulk polyadenylation do not underpin the molecular mechanisms by which MSUT2 and PABPN1 modulate tauopathy phenotypes.

Since poly(A) tails may influence specific mRNA stability, the consequences of knocking out MSUT2 on the mouse brain transcriptome by sequencing total RNA isolated from 2.5-month-old mouse brains was examined. Multidimensional scaling and principal component analysis revealed clustering of control and MSUT2 KO transcriptomic profiles (FIG. 7G). Overall, few transcripts exhibited robust changes in abundance with few mRNAs exhibiting significant changes in expression (n<70) and none greater than 2-fold except for MSUT2 (FIG. 7H, and Table 3). Likewise, surprisingly few genes exhibited differential exon inclusion with 201 significantly differentially spliced exons detected (FIG. 7I and FIG. 16 ). These data suggest MSUT2 mediates its effects on tau by mechanisms other than regulation of mRNA levels and certainly not through global changes in mRNA processing/stability as might have been expected for a bulk poly(A) binding protein. Because PABPN1 has been shown to have dramatic effects on alternative polyadenylation site selection (APA) during mRNA processing (M. Jenal, R. et al., Cell 149, 538-553 (2012)), APA was analyzed in the MSUT2 KO RNAseq data set using the Dynamic Analysis of Polyadenylation site by RNAseq (DaPars) (Z. Xia, et al., Nat Commun 5, 5274 (2014)) (FIG. 7J and FIG. 17 ). Unlike with PABPN1, depletion of MSUT2 has modest consequences for alternative PAS utilization with 10 mRNAs showing a significant change greater than the 20% threshold. By contrast PABPN1 knockdown caused significant changes in PAS utilization for 500 mRNAs over the 20% threshold with more than 200 mRNAs exhibiting greater than 2 fold changes in PAS utilization (M. Jenal, et al., Cell 149, 538-553 (2012)).

TABLE 3 MSUT2KO vs B6 RNAseq gene expression changes. log2Fold baseMean Change lfcSE pvalue padj symbol qvalue 7424.280841 −0.539509641 0.095463119 1.59E−08 1.44E−05 Zc3h14 9.03E−06 599.5610828 −0.478783463 0.098806015 1.26E−06 0.000589059 Col24a1 0.0003684 570.7311519 −0.432272958 0.10387244 3.16E−05 0.007716042 Fut10 0.004825644 2205.614241 −0.414000115 0.078574924 1.37E−07 9.14E−05 Ccnd1 5.71E−05 827.5027793 −0.401547526 0.106153071 0.000155123 0.029777616 Col5a1 0.018623044 497.8976194 −0.401488262 0.096534127 3.20E−05 0.007716042 Gm14169 0.004825644 4382.090393 −0.397366539 0.107393008 0.000215501 0.03708852 Tmem181b-ps 0.023195314 513.8788067 −0.394476199 0.106106486 0.000201014 0.035830738 Echdc2 0.022408692 6024.122224 −0.37875677 0.061798073 8.85E−10 9.93E−07 Insig1 6.21E−07 664.2482456 −0.375255184 0.10117301 0.000208043 0.03643307 Hist1h1c 0.022785393 2104.005103 −0.368895577 0.101403365 0.000274867 0.042590249 Col11a1 0.026636118 577.3146581 −0.367585083 0.095542921 0.000119412 0.023839492 Rlbp1 0.014909317 3549.896679 −0.326519332 0.061198781 9.53E−08 6.80E−05 Ints7 4.25E−05 1134.13249 −0.320968783 0.068423287 2.72E−06 0.001085911 Sdccag8 0.000679133 596.0447332 −0.319937836 0.08196146 9.48E−05 0.019313224 Col4a5 0.012078571 2965.307706 −0.309050733 0.048576371 1.99E−10 2.84E−07 0610037L13Rik 1.77E−07 1532.908809 −0.295691528 0.067343534 1.13E−05 0.003522958 Fam101b 0.002203272 1001.76825 −0.270718349 0.057149661 2.17E−06 0.000941335 Park2 0.000588715 1385.402801 −0.261612142 0.062956501 3.25E−05 0.007716042 Tek 0.004825644 1146.673265 −0.25969436 0.070528789 0.000231317 0.037241991 Mrps27 0.023291296 848.9705216 −0.257755122 0.052227209 8.00E−07 0.000443877 Gm43737 0.000277603 1187.938667 −0.243085618 0.054797471 9.16E−06 0.003153434 Zfp143 0.001972171 1607.541126 −0.232663608 0.046501601 5.63E−07 0.000330836 Slc18b1 0.000206907 1407.588104 −0.230537253 0.056966132 5.19E−05 0.011511787 Commd10 0.007199519 26282.21204 −0.174833573 0.046326692 0.000160698 0.030265712 Hsph1 0.018928302 2275.109515 −0.145509577 0.04057085 0.000335076 0.048474273 Sh3gl3 0.030316011 9143.676477 −0.141794486 0.032220265 1.08E−05 0.003473078 Epdr1 0.002172077 13031.79421 −0.099174239 0.027278654 0.000277336 0.042590249 Ankrd46 0.026636118 4692.67823 0.098919895 0.026588503 0.000198907 0.035830738 Tbce1 0.022408692 5413.94015 0.121018007 0.028856396 2.74E−05 0.007205889 Exoc1 0.004506593 7145.204705 0.166703703 0.037037584 6.77E−06 0.002501256 Dzip1 0.001564296 2687.409477 0.171621735 0.041724249 3.90E−05 0.009056902 Ercc5 0.005664224 2406.413066 0.176606375 0.047808256 0.000220705 0.037241991 Poc5 0.023291296 1104.737265 0.193779853 0.052594832 0.000229251 0.037241991 Wdhd1 0.023291296 1571.206192 0.207487449 0.057744095 0.000326612 0.047944717 Hmgb3 0.029984825 12423.89053 0.218133154 0.055001394 7.31E−05 0.015863157 Usp48 0.009920884 1924.774799 0.222966446 0.043733302 3.43E−07 0.000213788 Pus7 0.000133704 2859.833203 0.235787524 0.049963461 2.37E−06 0.000984786 Rrnad1 0.00061589 4193.643163 0.236063411 0.059913933 8.15E−05 0.016941816 Slc25a37 0.010595482 1222.660309 0.237198292 0.056295502 2.51E−05 0.006785039 Gsap 0.004243391 3070.5244 0.239698676 0.066134597 0.000289626 0.043803677 Grm3 0.027395001 4034.4514 0.239833331 0.049507075 1.27E−06 0.000589059 Narf 0.0003684 14377.96886 0.242869581 0.059842055 4.94E−05 0.011204071 Luc7l 0.007007072 2980.928589 0.251412239 0.046379413 5.93E−08 4.56E−05 Galnt11 2.85E−05 5407.856259 0.254967501 0.057447958 9.07E−06 0.003153434 Uba5 0.001972171 4639.736409 0.255130896 0.058271412 1.20E−05 0.003617646 Ncbp1 0.002262491 8456.080682 0.290539077 0.06816236 2.02E−05 0.005606337 Ddhd1 0.003506226 807.6112815 0.305268331 0.077225601 7.72E−05 0.01639514 Mtrr 0.010253589 2176.111327 0.333123305 0.046361834 6.71E−13 1.34E−09 Dtymk 8.37E−10 708.98509 0.335344396 0.076757293 1.25E−05 0.00366627 Mcm8 0.0022929 4140.058098 0.335749763 0.080220403 2.85E−05 0.007287832 Bhlhe41 0.00455784 2618.686344 0.343633478 0.093516538 0.000238246 0.03774879 Msantd2 0.02360825 4094.385388 0.351413417 0.063055696 2.50E−08 2.08E−05 Per3 1.30E−05 7437.394197 0.355381709 0.092892105 0.000130376 0.025517912 Zkscan2 0.015959008 4468.287414 0.377263518 0.077946702 1.30E−06 0.000589059 Sgk1 0.0003684 746.9202893 0.38103927 0.103256116 0.000224048 0.037241991 F2r 0.023291296 550.9681612 0.391402382 0.086432071 5.94E−06 0.002281308 Aaed1 0.001426739 849.9385594 0.398222191 0.092342156 1.61E−05 0.004604424 Fzd4 0.002879626 1882.609448 0.483551341 0.052828693 5.53E−20 2.76E−16 Atp13a4 1.73E−16 7196.4107 0.576432167 0.099806459 7.67E−09 7.66E−06 Zmym6 4.79E−06 2007.764341 0.590285711 0.096341969 8.96E−10 9.93E−07 Per2 6.21E−07 529.7213291 0.701047964 0.106387082 4.41E−11 7.34E−08 Mid1 4.59E−08 4077.552062 0.80115702 0.106038692 4.18E−14 1.04E−10 Zfp729a 6.52E−11 2408.607482 0.82297539 0.056874573 1.87E−47 1.87E−43 Ddb2 1.17E−43

MSUT2 overexpression synergizes with pathological tau causing premature death. To test whether MSUT2 overexpression can provoke tau pathology in the mammalian brain, human MSUT2 was expressed in the brains of tau transgenic mice using an adeno-associated virus (AAV) vector. An existing transgenic mouse line with mild and non-progressive tauopathy driven by high level pan-neuronal expression of wild type human tau (Tau4RTg2652) was used (J. M. Wheeler, et al., Acta neuropathologica communications 3, 33 (2015)). AAV serotype 9 encoded human MSUT2 was stereotaxically injected into the hippocampus of the mouse brain. The MSUT2 vector drives strong expression of MSUT2 throughout the hippocampus that includes both the normal nuclear distribution as well as abnormal distribution in the cytoplasm and within the neuronal processes (FIG. 9A-D). By one month post injection, sites with MSUT2 overexpression exhibit dramatic exacerbation of tau neuropathology, while injection of GFP encoding AAV does not exacerbate tauopathy (FIG. 10A). In contrast to pTau, MSUT2 overexpression does not impact total Tau abundance (FIG. 9E). Accumulation of pTau+ lesions in the CA1 is also accompanied by clear evidence of neuronal loss in associated projection regions, which is lacking in GFP AAV injected mice (FIG. 10B).

Neuroinflammation, as evidenced by activated microglia and reactive astrocytes, occurs in association with pathological tau in tauopathies including AD. It was examined whether MSUT2 overexpression exacerbates gliosis in response to pathological tau in the mild non-progressive Tau4RTg2652 mouse model of tauopathy. Profound neuroinflammatory changes in the hippocampi of MSUT2-overexpressing Tau4RTg2652 mice, including dramatically increased microgliosis as detected by IBA1 immunostaining was observed (FIG. 10C, FIG. 9F). Likewise, increased astrocytosis as detected by GFAP immunostaining occurs in MSUT2 overexpressing Tau4RTg2652 mice (FIG. 10D, FIG. 11A). To explore whether MSUT2 KO prevents the neuroinflammatory responses to tauopathy in the more severe PS19 mouse model, brain tissue was immunostained for markers of astrocytosis and microgliosis. Significantly decreased astrocytosis in MSUT2 KO/PS19 mice compared to PS19 mice with normal MSUT2 was observed (FIG. 10E, FIG. 11B). Furthermore, a trend towards decreased microgliosis as detected by IBA1 staining was also observed (FIG. 12A-C). However, MSUT2 KO mice appear to not be resistant to neuroinflammatory changes induced by an exogenous chemical trigger such as kainic acid (FIG. 13 ).

Neuronal depletion of the MSUT2/PABPN1 complex occurs in AD and predicts age at disease onset. To investigate the involvement of MSUT2 in a human disease, MSUT2 protein levels in postmortem human brain from normal and AD cases was examined. It was observed that in the frontal cortex of AD patients, MSUT2-positive neurons harbor pathological tau species without overt co-localization of nuclear MSUT2 protein and cytoplasmic tau deposits (FIG. 14A). To investigate how MSUT2 expression may influence tau pathology in AD, MSUT2 expression was characterized in a cohort of 32 AD cases by immunostaining (Table 4). In approximately half of the AD cases, dramatically diminished MSUT2 expression was observed compared to controls while the remainder exhibited control levels of MSUT2 expression (FIG. 14B). This difference is not due to differences in postmortem intervals (FIG. 12D, and Table 2). Next, the AD cases were classified into two groups: MSUT2 normal and MSUT2 depleted, on the basis of MSUT2 immunostaining. In the subset of AD cases with depleted MSUT2 protein, the number of MSUT2-positive neurons was dramatically lower.

TABLE 4 MSUT2 table of AD case information. Case ID NPDX AGE SEX ONS DU PMI CERAD Braak MSUT2 PABPN1 UWA244 AD 78 M 72 6 7:00 3 3 High High UWA447 AD 93 F 84 9 6:30 1 3 High High UWA536 AD 78 F 69 9 2:20 2 3 High High UWA650 AD 94 M 91 3 3:05 3 3 High High UWA677 AD 86 M 80 6 2:40 3 3 High High UWA730 AD 100 F 82 18 3:08 2 3 High High UWA763 AD 91 M 82 9 7:00 2 3 High High UWA771 AD 86 M 81 5 4:25 3 3 High High UWA797 AD 62 M 55 7 4:32 3 3 High High UWA1501 AD 77 M 71 6 6:32 3 3 High High UWA1518 AD 77 M 63 14 5:20 3 2 High High UWA1550 AD 94 M 82 12 4:25 3 3 High Low UWA2385 AD 86 F 76 10 8:32 3 3 High High UWA3556 AD 89 M 86 3 6:25 3 3 High High CNDR2045 AD 71 F 60 11 5:00 3 3 Low Low CNDR2142 AD 81 F 71 10 4:00 3 3 Low Low UWA342 AD 60 F 54 6 7:30 2 2 Low Low UWA343 AD 82 M 76 6 8:00 3 2 Low Low UWA450 AD 76 M 65 11 4:30 3 3 Low Low UWA519 AD 82 F 55 27 8:00 3 3 Low Low UWA681 AD 75 M 64 11 4:30 3 3 Low High UWA732 AD 89 F 82 7 5:23 2 3 Low High UWA1443 AD 84 F 76 8 4:47 3 3 Low Low UWA3554 AD 77 M 57 20 7:25 3 3 Low Low UWA6511 AD 90 F 76 14 6:23 3 3 Low High UWA6542 AD 70 F 76 8 5:00 3 3 Low Low UWA6589 AD 68 M 57 10 9:25 3 3 Low Low

To explore whether PABPN1 also varies in AD, PABPN1 expression was examined and depleted PABPN1 in neuronal nuclei from a subset of AD cases was observed (FIG. 14C, Table 2). Depletion of PABPN1 is significantly correlated with depletion of MSUT2 (Spearman correlation coefficient=0.71, p=0.0003, Table 2). These findings suggest depletion of the molecular complex containing PABPN1 and MSUT2 proteins bound to poly(A) RNA. To explore whether the co-depletion of PABPN1 and MSUT2 might influence clinical AD, the relationship between AD cases' age at onset and either MSUT2 or PABPN1 depletion from neuronal nuclei was examined. It was observed that AD cases with depleted brain MSUT2 protein levels exhibit a relatively younger age at AD onset (FIG. 14D). Likewise, AD cases exhibiting nuclear depletion of PABPN1 also exhibit a significantly earlier age of disease onset (FIG. 14E).

PABPN1 and MSUT2 complex (PMC) depletion exacerbates disease severity in AD. Previous investigations from others have demonstrated a clear relationship between pathological tau burden and severity of dementia (T. Gomez-Isla, et al., Ann Neurol 41, 17-24 (1997); and P. T. Nelson, et al., J Neuropathol Exp Neurol 71, 362-381 (2012)). However, it is unknown whether PMC depletion correlates with pathological neurodegenerative changes in AD. To further explore the relationship between PMC and severity of neuroinflammation, frontal cortex in the AD case collection was examined for markers of astrocytosis and microgliosis. A dramatic and significant decrease in astrocytosis in the cortex of PMC depleted AD cases was observed (FIG. 14F), consistent with the observations in MSUT2 KO/PS19 mice above (FIG. 10E, FIG. 11B). A parallel trend for decreased microgliosis is also evident in PMC depleted AD cases (FIG. 14G) and in MSUT2 KO/PS19 mice (FIG. 12A-C). Likewise, an increase in pTau burden in the PMC depleted cases (FIG. 14H) and increased neuronal loss detected by NeuN staining (FIG. 14I) was also observed. Note that loss of MSUT2 alone does not provoke neurodegeneration in the mouse brain (FIG. 3C), rather it may be the loss of the PMC as a complex with poly(A) RNA that exacerbates AD severity.

Discussion

Pathological accumulation of abnormal tau occurs in normal aging, and to a much greater extent in AD and other related tauopathies. Abnormal assembly of tau and other aggregating proteins represent a toxic gain of function disrupting neuronal proteostasis in neurodegenerative disease. In AD specifically, accumulation of tau-positive lesions drives cognitive decline and neuronal loss (T. Gomez-Isla, et al., Ann Neurol 41, 17-24 (1997); and P. T. Nelson, et al., J Neuropathol Exp Neurol 71, 362-381 (2012)). As described herein, it was tested whether MSUT2, the mammalian homolog of sut-2, plays a role in tauopathy disorders by determining neuronal susceptibility to pathological tau accumulation.

It was demonstrated that MSUT2 does influence tauopathy related phenotypes in mammals. MSUT2 knockout mice exhibit reduced accumulation of phosphorylated and aggregated human tau driven by a human tau transgene. Likewise, MSUT2 KO mice are protected from the cognitive impairment and neuronal loss caused by neuropathological tau species. MSUT2 KO mice are also protected from neuroinflammatory changes in response to tauopathy as indicated by reduced astrocytosis. In contrast, introduction of excess MSUT2 exacerbates normally mild and non-progressive tauopathy phenotypes caused by a wild type human tau encoding transgene. MSUT2 overexpression in both nucleus and cytoplasm causes significant elevation of pTau accumulation and drives loss of neurons. While MSUT2 possesses a nuclear export signal, it is not normally seen in the cytoplasm, suggesting MSUT2 mislocalization may drive pathological tau by a direct but possibly supraphysiological mechanism. Regardless, MSUT2 overexpression also exacerbates neuroinflammation, as markers of both microgliosis and astrocytosis are elevated in regions with increased MSUT2 protein. These findings in tauopathy mouse models reveal neuronal MSUT2 levels determine both accumulation of pathological tau species and neuronal vulnerability (FIG. 15A).

In the model systems described herein, the mechanism of MSUT2 modulation of tauopathy involves the nuclear RNA binding functions of MSUT2. It was demonstrated herein that MSUT2 binds both to poly(A) RNA and to another nuclear poly(A) binding protein, PABPN1. The results showed that MSUT2 and PABPN1 co-occupy poly(A) RNA localized to nuclear speckles, forming a macromolecular complex. Furthermore, the constituents of this complex become co-depleted in AD cases with earlier onset or more extensive tau pathology. Others showed that PABPN1 and MSUT2 have opposing effects on poly(A) tail length (S. M. Kelly, et al., RNA 20, 681-688 (2014); and S. M. Kelly, et al., Dev Neurobiol 76, 93-106 (2016)). The results show that MSUT2 and PABPN1 also function together to influence tauopathy. MSUT2 normally promotes tau aggregation while PABPN1 normally promotes clearance of aggregated tau. To test the linkage between RNA polyadenylation state and susceptibility to tauopathy, the predominant poly(A) nuclease in the C. elegans model of tauopathy was inhibited and the results show that increasing the poly(A) tail length does not ameliorate tauopathy. These findings implicate functions of MSUT2 and PABPN1 other than mediation of poly(A) tail length as an important control point in tau proteostasis.

How does the RNA binding function of MSUT2 impact tau pathology? It was initially thought that the loss of MSUT2 function ameliorated tauopathy via changes in gene expression. However, RNAseq analysis of MSUT2 knockout brain revealed limited changes in gene expression, alternative splices, or alternative polyadenylation site selection. Another hypothesis implicates RNA stress granules in the process of pathological protein aggregation whereby poly(A)+ mRNA becomes recruited to stress granules containing poly(A) binding proteins (N. Kedersha, et al., J Cell Biol 169, 871-884 (2005)). In AD, RNA stress granule assembly factors TIA1 and G3BP overlap with tau positive lesions in neurons (T. Vanderweyde, et al., Cell reports 15, 1455-1466 (2016); and T. Vanderweyde, et al., J Neurosci 32, 8270-8283 (2012)). TIA1 participates in RNA stress granule assembly, binds poly(A) RNA, and has similarity to other poly(A) binding proteins (Q. Tian, et al., Cell 67, 629-639 (1991); and A. Kawakami, et al., Proc Natl Acad Sci USA 89, 8681-8685 (1992)). Thus, one possible mechanism of MSUT2 action could be through promotion of stress granule formation leading to increased tau aggregation. Formation of tau/RNA coacervates or tau liquid-liquid phase separation, properties of known aggregation-prone RNA binding proteins, has recently been suggested as a mechanism for initiating tau fibrillization (S. Wegmann, et al., EMBO J 37, (2018); and ×. Zhang, et al., PLoS Biol 15, e2002183 (2017)). Another possible mechanism could involve a direct tau-RNA interaction whereby RNA, as a polyanion, can both sequester tau from its function as a tubulin binding protein and potentially promote pathological aggregation (X. Zhang, et al., PLoS Biol 15, e2002183 (2017); and J. B. Bryan, et al., Proc Natl Acad Sci USA 72, 3570-3574 (1975)). An alternative hypothesis incorporates the relationship between microtubule dynamics and polyadenylation. Previous work demonstrated that pathological tau causes microtubule hyper-dynamicity in tau transgenic mice (D. M. Barten, et al., J Neurosci 32, 7137-7145 (2012)). Tau pathology and consequent neurocognitive deficits can be ameliorated by stabilization of microtubules (K. R. Brunden, et al., J Neurosci 30, 13861-13866 (2010); B. Zhang, et al., J Neurosci 32, 3601-3611 (2012); and D. M. Barten, et al., J Neurosci 32, 7137-7145 (2012)). Previous investigation of the role of mRNA polyadenylation showed that defects in any one of several polyadenylation factors limits polyadenylation and causes MT destabilization or hyper-dynamicity (K. M. Cappell, et al., Mol Cell Biol 30, 5135-5144 (2010)). Thus, these data suggest that MSUT2 KO effects on polyadenylation may restore MT stability, thereby modulating tauopathy phenotypes (FIG. 15B).

While investigation of the molecular and cellular functions of MSUT2 has received attention in the context of RNA metabolism, investigation of its overall importance in brain function remains underdeveloped. However, its abundant expression in neurons suggests it may play a role in brain function. Recent reports implicate MSUT2 in learning and cognitive function in flies and mice (S. M. Kelly, et al., RNA 20, 681-688 (2014); S. M. Kelly, et al., Dev Neurobiol 76, 93-106 (2016); and J. Rha, et al., Hum Mol Genet, (2017)). Furthermore, the data described herein suggest MSUT2 may play an important role in mediating tauopathy-induced cognitive dysfunction. Nevertheless, the relationship between MSUT2 function, poly(A) RNA, and cognition remains unclear. The nuclear polyadenylation machinery and regulators of cytoplasmic mRNA polyadenylation also regulate synaptic function and memory (L. Du, et al., RNA 11, 1340-1347 (2005); and J. E. Kwak, et al., Proc Natl Acad Sci USA 105, 14644-14649 (2008)). For instance, the cytoplasmic polyadenylation element RNA binding protein (CPEB) possesses prion-like protein aggregation properties and influences poly(A) abundance and learning (K. Si, et al., Cell 115, 893-904 (2003)). Likewise, the RNA binding protein Cst-64 binds RNA and can influence learning and behavior in mice (J. C. Harris, et al., PLoS One 11, e0165976 (2016)). Collectively, poly(A) binding proteins and regulatory factors affect cognition and the co-depletion of MSUT2 and PABPN1 in AD suggests poly(A) binding protein homeostasis becomes disrupted in a substantial subset of AD cases.

In the human brain, MSUT2 protein occurs primarily in neurons. In AD cases, many tangle bearing neurons that are MSUT2 positive were observed. Extensive characterization of MSUT2 expression revealed that in about half of AD cases examined, MSUT2 protein becomes dramatically reduced. MSUT2 depletion occurs more often in AD cases with earlier onset and more extensive tau pathology, suggesting the possible loss of MSUT2+ neurons. In the same AD cases with depleted MSUT2, PABPN1 is also reduced suggesting depletion of the MSUT2/PABPN1 complex (PMC) occurs in earlier onset AD. While it is difficult to discern functional relationships between postmortem examination of pathological tau and underlying disease mechanisms, the data disclosed herein suggest that MSUT2+ neurons may die when challenged with pathological tau. Thus, cases with earlier onset AD could exhibit more extensive pathological tau and loss of MSUT2+ neurons while cases with later disease onset and milder tauopathy show a sparing of MSUT2+ neurons. The experiments overexpressing MSUT2 in mouse neurons demonstrated a dramatic exacerbation of tau pathology consistent with the notion that MSUT2 activity determines sensitivity to neuronal challenge by pathological tau.

While the relationship between tau pathology and neuroinflammation remains poorly understood, pathological tau clearly provokes neuroinflammation. Likewise, increasing neuroinflammation frequently exacerbates tauopathy. It remains less clear whether an adaptive form of neuroinflammation can mediate clearance of pathological tau and promote neuronal survival. Here, the data show that MSUT2 function promotes the brain's neuroinflammatory response to pathological tau. In mice, knockout of MSUT2 leads to a decrease in astrocytosis and microgliosis in tauopathy mice. Overexpression of MSUT2 in neurons provokes additional astrocytosis and microgliosis in tauopathy mice. Previous work showed that poly(A) can modulate inflammatory pathways (K. M. Rose, et al., Nature 267, 178-180 (1977)). Thus, MSUT2 function may drive susceptibility to tauopathy and gliosis by changing the neuroinflammatory response to tau pathology. Regardless, in AD patients, PMC+ cases exhibit a later disease onset in the face of a more robust neuroinflammatory response. Conversely, AD PMC-depleted cases exhibit an earlier disease onset but a weak neuroinflammatory response. Taken together, these observations suggest MSUT2 through the PMC could promote an adaptive neuroinflammatory response to AD neuropathology.

The work with MSUT2 demonstrates the molecular disease mechanisms of tauopathy remain conserved from C. elegans to humans. In mice, hypoactivity of MSUT2 protects neurons against abnormal tau while MSUT2 hyperactivity exacerbates tauopathy. Analysis of MSUT2 function implicates RNA polyadenylation machinery as an important node of cellular function in tauopathy. Likewise, the data presented here provides evidence that MSUT2 activity potentiates the neuroinflammatory response to pathological tau. Given the current dearth of success therapeutically targeting tauopathy, approaches targeting RNA processing warrant further investigation. Although how loss of MSUT2 protects against neurodegeneration requires further investigation, reducing MSUT2 function has potential as a therapeutic approach for treating tauopathies because complete loss of this protein appears to have little effect on mouse development or function. Described herein is MSUT2 as a therapeutic target for the development of small molecule inhibitors or specific reduction of gene expression by newly developed antisense oligonucleotide or CRISPR-based modulation of gene expression. Since tau accumulation in AD appears to occur concomitant with amyloid plaque deposition, it may be possible to stop the progression of neurodegeneration even after the Aβ-initiated AD process has begun by targeting tau through MSUT2.

Materials and Methods

Study design. The objective in conducting this study was to investigate the genetic and molecular involvement of MSUT2 in tauopathy. Previous work has suggested that MSUT2 expression modulates susceptibility to pathological tau in simple model organisms (C. R. Guthrie, et al., Hum Mol Genet 18, 1825-1838 (2009); C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011); and J. M. Wheeler, et al., Biochem Soc Trans 38, 973-976 (2010)). This work evaluated the impact of MSUT2 levels of pathological tau deposition in rodents and human AD patients. The mice (131 total mice) were on the C57BL/6J genetic background. MSUT2 KO mice were generated by KOMP using standard knockout mouse technologies (K. C. Lloyd, Ann N Y Acad Sci 1245, 24-26 (2011)). The PS19 transgenic mouse model expressing human P301S mutant human tau was utilized for its well characterized and highly progressive tauopathy related phenotypes (Y. Yoshiyama, et al., Neuron 53, 337-351 (2007)). A second, less severe tauopathy model was also chosen on the basis of its mild, consistent, and non-progressive tauopathy phenotype driven by wild type human tau (J. M. Wheeler, et al., Acta neuropathologica communications 3, 33 (2015)). Animals were assigned to experimental (MSUT2 KO) and control (MSUT2+/+) groups based on genotype. Experimental group sample sizes for neuropathology were based on previous pathological findings (Y. Yoshiyama, et al., Neuron 53, 337-351 (2007); and J. M. Wheeler, et al., Acta neuropathologica communications 3, 33 (2015)). FFPE tissue sections from each brain were collected using standard histological techniques (see below). For each experiment shown for mice, representative sections from each experimental animal were immunostained and visualized by standard light microscopy. Histology was analyzed under identical conditions for both experimental and control sections. Except where indicated, analyses were performed non-blinded using identical experimental procedures for both imaging and analysis. Where necessary, image adjustments applied linear contrast and brightness changes. For behavioral analysis, group sizes were based on previously published findings with these models (H. Takeuchi, et al., PLoS ONE 6, e21050 (2011); and J. M. Wheeler, et al., Acta neuropathologica communications 3, 33 (2015)). For RNAseq analysis, RNA isolated from brains of MSUT2 KO mice were compared with C57BL/6 mice. Brain specimens from a total of 27 Alzheimer's patients were subjected to histological and neuropathological analysis. AD autopsy cases were obtained from the UW ADRC and UPENN CNDR brain banks after standard neuropathological evaluation per NIAA criteria (T. J. Montine, et al., Acta Neuropathol 123, 1-11 (2012)). Evaluation of tissue specimens was conducted using the same workflows outlined for the rodent experiments above.

Construction of knockout mice. B6-Zc3h14^(tm1a(KOMP)Wtsi) mice were generated from a KOMP ES cell line (K. C. Lloyd, Ann N Y Acad Sci 1245, 24-26 (2011)). B6-Zc3h14^(tm1a) animals were crossed with strains carrying the Flp and Cre recombinases (12954/SvJaeSor-Gt(ROSA)26Sor^(tm1(WP)Dym)/J and B6.129S4-Meox2^(tm1(cre)Sor)/J, respectively) to remove exon 13 of the Msut2 gene as well as the inserted transgene sequences. PS19 animals (B6-Tg(Prnp-MAPT*P301S)PS19Vle) were backcrossed to C57BL/6 for >10 generations. Tau4RTg2652 tauopathy model mice were generated (J. M. Wheeler, et al., Acta neuropathologica communications 3, 33 (2015)). Briefly, the cDNA encoding the most abundant brain isoform (1N4R) of tau was cloned into a mouse neuron specific expression vector, pThy1.2 (T. Seki, et al., Proc Natl Acad Sci USA 82, 6657-6661 (1985)). Transgenic mice were generated by pronuclear microinjection of the Thy1.2::Tau (1N4R) transgene at the University of Washington Nathan Shock Center Transgenic Animal Model Core (Warren Ladiges, PI). Founder mice were intercrossed with C57BL/6J mice to establish lines. The Tau4RTg2652 line was the focus of characterization due to its high level tau expression and robust phenotype. Mice from the Tau4RTg2652 line used in these studies were backcrossed 10 generations (incipient congenic) with the C57BL/6J strain. This mouse strain has been deposited with the Mutant Mouse Regional Resource Centers (MMRRC) and is available under the stock number MMRRC:036717 and the strain name of B6.Cg-Tg(Thy1-MAPT*)2652Gds.

Immunohistochemistry and histological stains. Immunohistochemistry was performed on paraffin embedded frontal cortex sections from over 30 AD cases. In addition, the following transgenic mouse lines were examined by immunohistochemistry: 9 month-old PS19 Tg mice (n=24), MSUT2 KO/PS19 Tg mice (n=24), 4 month old Tau4RTg2652 mice injected with AAV-MSUT2 (n=15) or AAV-GFP (n=5). Mice were anesthetized and fixed by transcardial perfusion with 4% paraformaldehyde. Brains were removed and paraffin embedded for sectioning. Coronal sections from the hippocampus were cut and stored at 4° C. until use. Human and mouse brain sections were deparaffinized and rehydrated through alcohols and an antigen retrieval step consisting of heat pretreatment by microwave or autoclave in citrate buffer was used when necessary. Sections were treated for endogenous peroxidases with 3% hydrogen peroxide in PBS (pH 7.4), blocked in 5% non-fat milk in PBS, and incubated with one of the following primary antibodies overnight at 4° C.: MC1 (G. Carmel, et al., J Biol Chem 271, 32789-32795 (1996)), AT180 (ThermoScientific, catalog MN1040), GFAP (Dako Cytomation Z0334), Iba1 (Wako 019-19741), MSUT2 (C. R. Guthrie, et al., Hum Mol Genet 18, 1825-1838 (2009)), PABPN1 (Abcam ab81224), tau (Rb17025, (T. Ishihara, et al., American Journal of Pathology 158, 555-562 (2001)), or NeuN (Millipore MAB377). Biotinylated secondary antibody was applied for 45 min at room temperature. Finally, sections were incubated in an avidin-biotin complex (Vector's Vectastain Elite ABC kit, Burlingame, Calif.) and the reaction product was visualized with 0.05% diaminobenzidine (DAB)/0.01% hydrogen peroxide in PBS. Negative controls with secondary antibody alone did not immunostain tissue sections. The presence of NFTs was assessed by Gallyas silver staining (A. Y. Sun, et al., Journal of Histochemistry & Cytochemistry 50, 463-472 (2002)). In addition, cresyl violet staining was performed to assess neuronal loss.

For double label immunofluorescence of AT180 and MSUT2 in human AD brain, AlexaFluor 488 goat anti-rabbit and AlexaFluor 594 goat anti-mouse secondary antibodies (Molecular Probes) were used and autofluorescence was quenched with 0.1% Sudan Black.

For quantitation, stained sections were analyzed using the computerized image analysis system, MicroComputer Imaging Device (MCID, Imaging Research, St. Catherines, Ontario, Canada). Blinded assessment of optical density measurements were obtained relative to the proportional area for AT180, MC1, GFAP, Iba1, NeuN and cresyl violet staining in frontal cortex and hippocampus. Data were averaged and are represented as mean+/−SEM. A two tailed Student's t-test was used to assess differences in staining intensity between experimental groups.

Photomicrography and figure preparation. Immunohistochemistry photomicrographs were taken with a digital camera and imported into Adobe Photoshop. To optimize visualization of staining, photomicrographs were modified when necessary by adjusting brightness and contrast. Fluorescent and immunofluorescent microscopy was performed on a Delta Vision microscope (GE, Inc) using a 60× oil immersion objective, a sCMOS camera, and 2×2 binning. Image analysis was performed using softWoRx 6.0 Beta software (GE, Inc).

Rodent behavioral analysis. Mice were bred and housed at the VAPSHCS animal facility, and all experiments were approved by the IACUC committee. Mice were housed on a 12:12 light cycle in static microisolator cages, with rodent chow and water available ad libitum. Environmental enrichment was added at every cage change. The behavioral experiments were conducted during the light phase.

Open field testing was conducted in a 30 inch diameter circular plastic arena. The animals were moved into the testing room approximately 1 hour prior to start of testing. The arena was cleaned with 70% ethanol between animals. Total locomotor activity was measured for 10 min using SMART behavioral tracking system (San Diego Instruments).

The Barnes maze is a circular white plastic platform 36 inches in diameter with 20 holes around the perimeter. One hole leads to a dark target escape box containing clean bedding material. Latencies to locate and to enter the escape box were recorded. Spatial cues (blue circle, yellow triangle, black/white striped square) were placed around the maze to be used as landmarks to find the escape box. Mice are placed in a clear box in the center of the maze for 30 sec at the beginning of each trial, so the direction each mouse faces at the trial start is random. When the start box is removed, each animal has a maximum of 2 min to locate the escape box. If the animal locates the hole, it is allowed to shelter there for 1 min before being returned to the home cage. If the animal fails the task, it is gently guided to the escape box by the investigator and allowed to shelter there for 1 min. The animals were moved into the testing room approximately 1 hour prior to start of testing, and the maze was cleaned with 70% ethanol between animals. Training trials were conducted twice daily on two consecutive days.

Rotorod testing was conducted using an accelerating UGO Basile Rota Rod. The rod surface is covered with ridged plastic, located 18 inches above a padded floor. The mice were transferred to the testing room approximately 1 hour prior to the start of testing, and were tested on four consecutive days. On the first three days, the mice received three training trials separated by a minimum of 30 min rest time. Animals were placed onto a stationary rotorod and allowed to acclimate for a minimum of 10 seconds before accelerating the rod up to 8 rpm over 2 minutes on all training trials. On the final test day, the animals were tested in four trials with acceleration up to 8, 16, 24, and 32 rpm.

Cell Culture, RNA interference, & transient transfections. HEK293 and HEK/tau cells (100 μg/ml Zeocin) were cultured under standard tissue culture conditions (DMEM, 10% defined fetal bovine serum, Penicillin (1000 IU/mL) Streptomycin (1000 μg/mL) (C. R. Guthrie, et al., J Mol Neurosci 45, 32-41 (2011); and C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011)). RNA interference and plasmid transient transfections were conducted following manufacture's protocol (RNAiMAX, Invitrogen).

Immunofluorescent staining and fluorescent in situ hybridization, Cells were grown on poly-D-lysine coated 12 mm round coverslips and fixed in 4% formaldehyde solution. Cells were washed 3×5 min in PBS/Ca²⁺/Mg²⁺, then blocked in antibody buffer (PBS, 0.5% Triton X-100, 1 mM EDTA, 0.1% BSA, 0.05% NaN₃) with 10% normal goat serum. Primary antibodies were applied and incubated for 1 hour at room temperature. Primary antibodies used were: PABPN1=Proteintech Group (Catalog #10782-2-AP), MSUT2=Rabbit 9857-2-AP (C. R. Guthrie, et al., Hum Mol Genet 20, 1989-1999 (2011)), oligomeric tau=TOC1 (S. M. Ward, et al., Biochem Soc Trans 40, 667-671 (2012)), SC35=Sigma Aldrich (Catalog #S4045). Cells were washed 3×5 min in PBS/Ca²⁺/Mg²⁺, then re-blocked for 10 min. Appropriate Alexa dye-labeled secondary antibodies (Invitrogen) were applied and incubated for 20 min at room temperature. Cells were again washed 3×5 min in PBS/Ca²⁺/Mg²⁺, counterstained with 300 nM DAPI and mounted with ProLong Gold antifade (Molecular Probes). TOC1 staining was conducted with 10% rabbit serum in antibody buffer. Rabbit anti-mouse secondary antibody used for TOC1 was FITC labeled (Invitrogen). Fluorescence In Situ Hybridization was conducted prior to counterstaining with DAPI as per the following: After secondary antibody staining, cells were washed 3×5 min in PBS/Ca²⁺/Mg²⁺, 100 μg/μl 5′ Alexa-647 labeled Poly(T) oligonucleotide (sequence=TTTTT TTTTT TTTTT TTTTT TTTTT TTTTT TTTTT TTTTT TTT (SEQ ID NO: 23); IDT), and incubated in the dark for 2 hrs at 37° C. Following hybridization, the samples were washed once in PBS/Ca²⁺/Mg²⁺ in the dark for 30 min at 37° C. Proximity Ligation assays were preformed using Duolink PLA technology (Sigma Aldrich Catalog #DUO92101). Human brain samples stained for MSUT2 and PABPN1 were imaged on a Leica TCS SP5 II confocal microscope using a 63× oil immersion objective. Colocalization analysis of confocal images were conducted in ImageJ 1.51n using Coloc 2 (J. Schindelin, et al., Nat Methods 9, 676-682 (2012)).

Recombinant protein purification & in vitro binding assays. The MSUT2 ZF and PABPN1 protein expression constructs were prepared by inserting the MSUT2 ZF or PABPN1 cDNA into the pGEX6P-1 expression vector (Pharmacia) to generate a construct encoding a Glutathione S-Transferase (GST)-MSUT2 ZF or GST-PABPN1 fusion protein. The GST moiety allows one step affinity purification of recombinant protein on Glutathione coupled sepharose beads. A log phase culture of BL21 (DE3) cells carrying the pGEX-MSUT2 or PABPN1 vector was induced for 3 hours at 37° C. with shaking. E. coli lysates were treated with benzonase nuclease which degrades both RNA and DNA prior to clearing and purification. Glutathione sepharose (Pharmacia) was used as the affinity resin and purified (J. V. Frangioni, et al., Anal Biochem 210, 179-187 (1993)). In vitro protein-binding assays were performed using ³⁵S labeled PABPN1 protein generated with TNT reticulocyte lysates (Promega, Inc); labeled PABPN1 was pretreated with RNAse (B. Kraemer, et al., Curr Biol 9, 1009-1018 (1999)). Briefly, GST beads coupled to MSUT2 were blocked and then incubated with labeled PABPN1 both of which had been pretreated with nucleases to remove RNA. Unbound protein was repeatedly washed away and then labeled proteins were eluted by boiling and analysis on SDS-PAGE.

Behavioral assay in C. elegans. Cultures were maintained at 20° C. on standard 60 mm NGM plates containing OP50 Escherichia coli (S. Brenner, Genetics 77, 71-94 (1974)). A timed egg lay using 10-20 gravid adults was performed and worms grown for 4 days at 20° C. To assess swimming behavior, a plate containing a synchronized population of worms was flooded with 1 mL of M9 buffer. The M9 solution containing C. elegans was pipetted onto an unseeded 35 mm NGM plate. One minute after the addition of M9 buffer, swimming worms were recorded using WormLab (MBF Bioscience) for 1 minute at 14 frames per second. Videos of swimming worms were analyzed using WormLab 2017 software. Swimming behavior was quantified by measuring the number of turns made by a worm during the video. A turn was calculated using Bending Angles-Multiple and setting the sample angles to 3, the amplitude threshold to 20°, and the duration threshold to 2 frames (0.14 seconds). Data from the angle 2 (the angle made from the body quarterpoints and midpoint) was used. The number of turns a worm made was divided by the time a worm was tracked by the software to calculate turns per minute. Only worms that were analyzed for at least 20 seconds were kept in the analysis. At least 100 worms were analyzed per strain.

RNAseq analysis. Raw reads from RNAseq experiments had their 3′ Illumina TruSeq Indexed adaptors (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; SEQ ID NO: 24) trimmed using cutadapt v1.8.3 with parameters “-e 0.06 -O 6 -m 14 -n 2 --length-tag “length=”” (M. Martin, Cutadapt Removes Adapter Sequences From High-Throughput Sequencing Reads. http://dx.doi.org/10.14806/ej.17.1.200 17). Reads were then mapped to the mm10 Mus musculus genome build using STAR version 2.4.1d with parameters “--outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --outFilterMismatchNoverReadLmax 0.06” (A. Dobin, et al., Bioinformatics 29, 15-21 (2013)) and were further filtered to mapping reads with a maximum mismatch rate of 0.06. The mapped reads from the RNA sequencing pipeline were analyzed for differential expression by using HTSeq with parameters “-s reverse -t exon -i gene id” (S. Anders, et al., Bioinformatics 31, 166-169 (2015)) to compute the number of reads mapping to each gene using Ensembl mm10 gene annotations (F. Cunningham, et al., Nucleic Acids Res 43, D662-669 (2015)). Gene counts were then analyzed for differential expression with the DESeq2 R package v1.0.19 (M. I. Love, et al., Genome Biol 15, 550 (2014)). Splicing analysis was performed using the DEXSeq R package (S. Anders, et al., Genome Res 22, 2008-2017 (2012)). Briefly, exon reads were counted using the dexseq_count.py script and read into R v3.0.1 (R. D. C. Team, R: A language and environment for statistical computing. R Development Core Team (2011), R: A Language and Environment for Statistical Computing. Vienna, Austria: the R Foundation for Statistical Computing. ISBN: 3-900051-07-0. Available online at http: www.R-project.org/), where the DEXSeq analysis pipeline was followed using the GENCODE mm10 genome annotation. For both the differential expression and the differential splicing analyses, significantly differentially expressed genes/exons were defined as having an adjusted p-value of less than 0.05 using the Benjamini-Hochberg multiple testing correction (Y. B. a. Y. Hochberg, Journal of the Royal Statistical Society. Series B (Methodological) 57, 289-300 (1995)).

Alternative polyadenylation analysis. To perform alternative polyadenylation analysis, the DaPars tool was used (Z. Xia, et al., Nat Commun 5, 5274 (2014)). Ensembl gene annotations for the mm10 Mus musculus genome were downloaded from the UCSC Table Browser (W. J. Kent, et al., Genome Res 12, 996-1006 (2002)) and the DaPars_Extract_Anno.py script was used to generate 3′ UTR annotations. Then, the RNA-seq data was converted to BedGraph format using the bedtools genomecov command (A. R. Quinlan, et al., Bioinformatics 26, 841-842 (2010)). Finally, the DaPars_main.py script was used to perform the alternative polyadenylation analysis.

Surface plasmon pesonance. SPR experiments were conducted on a Biacore T200 using the Biotin Capture Kit Series S following the manufacturer's instructions (GE). Biotin capture reagent was applied to the sensor chip at a flow rate of 2 μl/minute for 300 seconds. lnM biotinylated RNA (BiotinTEG-AAAAAAAAAAAAAAA; SEQ ID NO: 25) was captured at a flow rate of 10 μl/minute for 180 seconds. Samples were flowed across the sensor chip at 50 μl/minute for 120 seconds and the chip was regenerated for 120 seconds at a flow rate of 10 μl/minute. K_(D) values for binding and disassociation were calculated from the binding kinetics of each protein at five concentrations using the Biacore T200 Software v3.1 application package (GE; 1, 0.9, 0.8, 0.7, 0.6 μM).

Immunoblotting. Tau fractions were obtained (B. C. Kraemer, et al., Proc Natl Acad Sci USA 100, 9980-9985 (2003)). Protein samples were brought to 10 mM Tris, pH 6.8, 1 mM EDTA, 40 mM DTT, 1% SDS, 10% sucrose by addition of 5× sample buffer boiled 5 minutes and loaded onto 4-15% pre-cast criterion SDS-PAGE gradient gels (Bio-Rad). For immunoblotting, human tau was detected using antibody 17025 at a dilution of 1:6000 (C. R. Guthrie, et al., Hum Mol Genet 18, 1825-1838 (2009)). Anti-tubulin antibody was used at a dilution of 1:1000 (Developmental Studies Hybridoma Bank, catalog E7). MSUT2 antibody Rbt9857 was prepared as described herein and used at a dilution of 1:1000. Secondary goat anti-mouse or goat anti-rabbit IgG were the secondary antibody reagents used at a dilution of 1:1000 (GE Lifesciences). Signals were measured by densitometry using Adobe Photoshop.

Stereotaxic injections of AAV viral vector. AAV viral vector preparations expressing either MSUT2 or GFP under control of the chicken beta actin promoter were obtained from Dr. Ronald Klein at Louisiana State University. Intracerebral injections were performed using a stereotaxic apparatus (Parkland Scientific) (P. Szot, et al., Frontiers in pharmacology 3, 184 (2012)). Three month old male and female Tau4RTg2652 mice were anesthetized with isoflurane and received a single injection of buprenorphine SR (0.3 mg/kg) during surgery for extended pain relief support. The animals received a single unilateral injection of 1.0 μl AAV9 (containing approx. 5×10E11 viral vectors) into the right ventral hippocampus delivered over an 8 minute period at the following coordinates: AP: −2.92 mm from bregma: ML: +2.80 mm; DV −3.50 mm from the surface of the skull. The needle was left in place for an additional 4 min after the injection and then the needle was slowly withdrawn. Animals were sutured, removed from the stereotaxic apparatus and allowed to recover. Animals were sacrificed 1 month later for analysis of neuropathological changes.

Human tissue. Samples of postmortem tissue from the University of Washington Alzheimer's Disease Research Center (ADRC) Neuropathology Core was used. AD cases were selected on the basis of having an autopsy-confirmed diagnosis of AD (Braak stages V or VI with CERAD score of moderate or frequent). Control samples were from neurologically healthy control participants, who were of a similar age with low levels of AD pathology (Braak stage III or less and CERAD scores of none or sparse).

Statistical analysis. Standard ANOVAs or t tests were used (two-tailed) for statistical analysis. Statistical analysis was performed using the Statistica software package (StatSoft). For measures, sex was included as a factor in the ANOVA. If sex did not have a significant effect on a particular measure, then the analysis was repeated without that factor. For repeated measures (Rotorod and Barnes testing), ANOVA was followed up with planned comparisons of the two genotypes on each testing day.

Example 2. High-Throughput AlphaScreen Assay

To identify small-molecule inhibitors of the MSUT2 protein/poly(A) RNA interaction, a high-throughput AlphaScreen assay optimized for detecting recombinant GST-MSUT2 binding to synthetic poly(A) RNA. The MSUT2 AlphaScreen assay has been well optimized during its development for 384-well screening (z-score=0.96). Two high throughput AlphaScreens of 53,400 distinct small molecules have been completed. A multi-point dose analysis pilot screen of the Spectrum Collection was performed. From this screen of ˜2,400 compounds, 20 preliminary hits with activity against MSUT2 were identified (FIG. 18 ) and showed robust dose validation for several (FIG. 19 ). Both the pilot screen and the screening approaches disclosed herein use the Quellos High-Throughput Screening Core at the University of Washington (UW).

Assay of inhibitor dose dependence. Hits identified in the pilot screen were validated by retesting resynthesized compounds over a wide concentration range. FIG. 20 shows a representative-dose response curve for Ebselen, which was one of the top hits in the pilot screen. These hits will be validated by conducting a 14-point dose-response analysis with a drug concentration range from 100 μM down to 1.4 nM; the MSUT2/poly(A) RNA AlphaScreen Assay will be used to produce a readout. From this dose-response analysis, IC50 values will be calculated for dose-responsive hits. For the full scale screen 64 primary hits were identified and will be subject to dose validation as described for pilot screen compounds (and Ebselen, shown in FIG. 20 ). It is expected that approximately one third of compounds from the primary screen will be validated based on the results from the pilot screen (6/20 hits showed robust dose validation and an IC50 below 20 μm).

Rigorous assessment of compound selectivity for MSUT2 over PABPN1. Hits identified in the primary screen will be validated by being retested over a 14-point dose range of drug concentrations from 100 μM to 1.4 nM; these methods will be identical to the dose validation of hit compounds in the pilot screen except using recombinant PABPN1 instead of MSUT2 (i.e., via a PABPN1/poly(A) RNA AlphaScreen assay). From this dose-response analysis, IC50s against both MSUT2 and PABPN1 binding to poly(A) RNA will be calculated. Although PABPN1 does not exhibit as robust a poly(A) RNA binding response by AlphaScreen or affinity (as measured by SPR), it will give a sufficient signal in the AlphaScreen assay to be measured in the same way as MSUT2/poly(A) RNA. Compounds that specifically inhibit MSUT2 but not PABPN1 RNA binding and that exhibit an IC50 <5 μM against MSUT2 will be given preference for characterization (FIG. 21 ).

Evaluation of inhibitor affinity for MSUT2 and poly(A) using surface plasmon resonance (SPR). Given that poly(A) performs many important functions in the cell, the goal is to disrupt the binding of MSUT2 to poly(A) RNA without interrupting the poly(A) interactions with PABPN1 or other poly(A)-binding proteins. Because CCCH domains can bind both RNA and protein, the MSUT2 association with poly(A) RNA was measured using a SPR assay; this demonstrated that MSUT2 affinity for poly(A) is about 4-fold greater than the affinity of PABPN1 for poly(A) (FIG. 22 ). Compounds will be tested to determine whether they directly associate with poly(A) RNA, PABPN1, or MSUT2. Hits that exhibit a high affinity for MSUT2, but not poly(A) RNA or PABPN1, will be advanced for further study.

Example 3: ALPHA Assay for MSUT2 Binding to Poly(A)

The steps and set up for performing the ALPHA assay for MSUT2 binding to polyA are as follows:

-   -   1. Dilutions are in assay buffer (1×PAMA final concentration).     -   2. Scale is for 96 well assay in PE 06 well 12 area plate (total         volume/well is 50 μL).     -   3. Assays set up in low light conditions     -   4. Add 20 μL of diluted donor bead (10 ug/mL) to well bringing         well volume to 20 μL     -   5. Add 10 μL diluted biotin RNA (15 nM)) bringing well volume to         30 μL     -   6. Add 10 mL diluted GST-MSUT2 Protein (125 nM)) bringing well         volume to 40 μL     -   7. Incubate at room temp for 30 minutes in the dark     -   8. Add 10 μL of diluted Acceptor bead (2.5 μg/mL) to well         bringing well volume to 50 μL     -   9. Incubate at room temp for 60 minutes in the dark     -   10. Read Plate using standard AlphaAssay settings on Perkin         Elmer EnSpire® Alpha microplate reader

Table 5 provides the reagents useful for carrying out the ALPHA assay for MSUT2 binding to polyA.

TABLE 5 Reagents. Composition and Final Concentration in Amount Reagent Assay Supplied Storage Assay 1 × PAMA: 400 mL of 10 × −20° C. Buffer 25 mM HEPES. 100 mM NaCl. 0.04% stock Casein. 1 mg/mL Dextran-500, 0.2% Triton X-100. pH 7.4 Donor PE Avidin AlphaScreen Donor (catalog ~3 mL 4° C.—do not Bead 6760002) at 4 ug/mL (@ 5 mg/mL) freeze Biotin- 5’ TEG-Biotin-Poly(A)20 RNA, 100 uM ~200 uL, −70° C.— RNA (660 ug/mL)—from IDT 100 uM Freeze/thaw OK MSUT2 GST-MSUT2 protein 50 nM (2.1 ~2 mL (2 × 1 mL, −70° C.— Protein mg/mL)—brownish 1 × 0.5 mL, 1 × 0.1 Freeze/thaw mL aliquots) decreases activity (@ ~2 mg/mL) Acceptor PE Glutathione AlphaLISA ~1 mL 4° C.—do not Bead Acceptor(catalog AL109C) at 0.5 μg/mL (@ 5 mg/mL) freeze

Example 4: Fluorescence Polarization/Anisotropy to Measure Binding

Fluorescence polarization/anisotropy (FP) is a technique used to measure binding between two biological molecules, often protein and ligand. As disclosed herein, are methods of using an FP screen capable of detecting mammalian SUT-2 (MSUT2) protein and fluorescein labeled 15-repeat polyadenylic RNA (FAM-polyA₁₅) interaction for the discovery of inhibitors. Briefly, FP assays rely on the fact that an excited fluorophore will emit polarized light inversely proportional to its rotational velocity. In terms of this assay, unbound FAM-PolyA₁₅ will emit depolarized light, however, when bound to MSUT2, the apparent molecular weight of the complex increases, lowering rotational velocity and increasing polarized light emission. Inhibitors blocking this interaction will cause rapid tumbling of FAM-PolyA₁₅ and subsequent decrease in polarized light emission (FIG. 23 ).

The results described herein show that bound MSUT2:FAM-PolyA₁₅ indeed emits polarized light in a dose dependent manner (FIG. 24A). Because the focus is screening for inhibitors of MSUT:FAM-PolyA₁₅ interactions, and not the important partner RNA-binding protein PABPN1, compounds were counter-screened for specificity against PABPN1:FAM-PolyA₁₅ interactions. A proof-of-concept experiment shows that FP is suitable to measure PABPN1:FAM-PolyA₁₅ interaction (FIG. 24B). Interactions between both MSUT2 and PABPN1 with PolyA can be inhibited by titrating unlabeled-PolyA, subsequently showing a decrease in emitted polarized light (FIG. 24C). Finally, results indicate that FP can be used to detect inhibitor specificity as compound A disrupts MSUT2: FAM-PolyA₁₅ binding, but not PABPN1: FAM-PolyA₁₅ (FIG. 24D). 

1.-89. (canceled)
 90. A method of screening for compounds capable of inhibiting MSUT2 binding to poly(A) RNA, the method comprising: (a) introducing at least one candidate compound into a mixture, wherein the mixture comprises poly(A) RNA, PABPN1, and MSUT2; (b) incubating the mixture under conditions in which PABPN1 is capable of stimulating RNA polyadenylation in the absence of the candidate compound; (c) determining whether the candidate compound inhibits MSUT2 binding to the poly(A) RNA by measuring RNA polyadenylation of the poly(A) RNA, wherein absence of RNA polyadenylation indicates that the candidate compound inhibits MSUT2 binding to poly(A) RNA; and (d) selecting the candidate compound which inhibits MSUT2 binding to poly(A) RNA.
 91. The method of claim 90, further comprising purifying the selected candidate compound.
 92. The method of claim 90, further comprising isolating the selected candidate compound.
 93. A method for screening compounds for pharmacological intervention in tauopathy disorders, the method comprising: (a) introducing at least one candidate compound into a mixture, wherein the mixture comprises poly(A) RNA, PABPN1, and MSUT2; (b) incubating the mixture under conditions in which PABPN1 is capable of stimulating RNA polyadenylation in the absence of the candidate compound; (c) determining whether the candidate compound inhibits MSUT2 binding to the poly(A) RNA by measuring RNA polyadenylation of the poly(A) RNA, wherein absence of RNA polyadenylation indicates that the candidate compound inhibits MSUT2 binding to poly(A) RNA; and (d) selecting the candidate compound which inhibits MSUT2 binding to poly(A) RNA.
 94. The method of claim 93, further comprising purifying the selected candidate compound.
 95. The method of claim 93, further comprising isolating the selected candidate compound. 